Definitely getting harder to breeze, I wrote in my notebook, and didn't notice I hadn't put ¨breathe¨ until later, when we had dropped 1,000 metres or so and my harassed red-blood cells had brought a little more oxygen to my brain. I was crouching in a pinkish-brown field of stones at the top of the Pata Pampa pass, about 4,800 metres above sea level. The wind blew cold and constant through the little pebble stupas piled up by travellers as offerings, but turned insubstantial when I tried to suck it in; I couldn't fill my lungs with it. Taking the few steps up from the road had made me pant, and the most comfortable way to look at the latest of today's strange views seemed to be down on my heels, squinting out of one eye at the far peaks topped with tiny glaciers like dribbles of frozen saliva, and at the Martian plateau where the road went next, among red rubble and cushions of moss the colour of a snooker table. I had to work hard to move the pen. The Quechua-Indian ladies down at the curve in the road included me in their impassive gaze.

They were waiting with bundles of knitwear for tourist buses to come by; meantime, here was the world, and here was panting gringo in its foreground. Their cheeks all had a blush at the point of the bone, a little blotch of red against their copper-brown skin - the sign of blood cells multiplied to cope with the altitude.

Pata Pampa was the highest point I reached in Peru, after a long morning's drive from the southern city of Arequipa through landscapes that scrambled my idea of what's supposed to happen when you climb a mountain range. We began on slopes of bone-dry with canyons and gulches dotted with spaghetti-western cactuses in the shape of giant candelabra. But above that came a volcano-rimmed plain of short golden-grass tussocks, where family groups of the llama's lithest little relative, the vicuña, lollopped delicately along. And then, the air thinning, beyond ramparts of wind-carved pumice, we entered a domain of long switchbacks across giant slopes of scree, with water trickling down under the stones. Wherever the land was flat enough, the water puddled into miniature wetlands, shining silver and peaty brown. Suddenly, at the top of the world, we were crossing a baby marsh, a laguna , thronged with leggy ibises, darting lapwings and geese, presumably taking a break from their long flap to the Pacific. None of this corresponded to the sequence familiar from European and North American mountains, where a green fertile world turns gradually cold and white. The Andes in Peru are too dry and too near the equator. There is a snowline, but in many areas it is not until almost 6,000 metres up, leaving the snow as a distant, congealed presence, restricted to the highest peaks.

Otherwise the mountains are a staircase of big, bare spaces, one after another, each with its own tenacious and peculiar ecology. Even on the cracked rock beyond Pata Pampa, where you'd think nothing would be at home but NASA astronauts in training, flop-eared chinchillas somehow contrive to live. They watched me from the boulders as I got out of the car a few miles further on, feeling the effect of all the coca tea I'd drunk as a tonic against the altitude, It's clear green infusion like a mint tea with a faint chalky edge. It certainly eases your lungs, but it's also a very effective diuretic.

I'd come to Peru, like the majority of visitors to the country, to see Machu Picchu - ´the heights of Machu Picchu´ as I thought of them, because of the great Pablo Neruda poem of that name. Entonces en la escala de la tierra ha subido... hasta ti, Machu Picchu (¨then up the ladder of the earth I climbed, until I reached you, Machu Picchu.´) Naturally, I imagined the lost city of the Inca emperors as being the furthest into the sky I'd get, the crowning glory of all Peru's altitude. And I wasn't wrong to suppose that the romance of the vertical is much of what makes Machu Picchu astonishing. In a country of heights, a country dedicated to all the possibilities of vertigo, it's the place that makes the most beautiful and artful use of height. However, in terms of absolute metres and centimetres above sea level, Machu Picchu is not that high. Instead of on the dry central spine of the Andes that runs all the way up Peru from south to north, it lies on the subsiding eastern side of the mountains, where the range has begun to drop down towards Brazil and the jungle basin of the Amazon. You get to it by descending a little way, by going a few rungs lower on the ladder of the earth. Like that of many travellers, my visit to Peru had been constructed to give me an inoculating dose of the really high country first, so that I could get any problems with headaches or nauseas out of the way early. By the time I started the journey to the ruins of Machu Picchu I ´d acclimatized, and when I arrived, the air there, down at 2,490 metres, seemed rich and soupy and positively luxurious to inhale. Ah, oxygen.

The journey began at Cusco, the old capital of the Inca Empire, and as alive a city as Machu Picchu is dead. Unlike Tenochtitlán, the metropolis of the Aztecs up Mexico, it wasn't wiped away when the conquistadores arrived and replaced by a completely Spanish city. Francisco Pizarro, conqueror of the Incas, was just as much of thug as Hernán Cortés, conqueror of the Aztecs; but although he stripped Cusco of gold and enslaved and abused its people, he left, despite himself, far more of the physical fabric of Incas civilisation. I could read the story of the city in the join between two rows of masonry. At about head height on a wall inside the present-day Church of St. Dominic, the black basalt blocks of the Incas' Temple of the Moon - huge things slotted together with hairline precision - become the base for a baroque arch: two civilizations fitted together with a literal seam, creating a fusion quite as weird as if a 16 th -century Spanish convent had been cemented onto Stonehenge, or the Pyramid of Cheops in Egypt.

Inca civilization was smashed but not discarded. The bits were used again, like one of those stained-glass windows made from fragments of older stained glass, where eyes and hands and gargoyle tails turn up in unexpected conjunctions. The conquistadores turned the temples into churches, and stole for themselves the block-long palaces where the descendants of each dead emperor reverently tended his mummified body. But they used the stonemasons of the Incas to do the work.

The narrow streets of central Cusco still follows the shape on the ground of a stylized puma, its head pointing to the titanic stone ramparts of Sacsayhuaman on the ridge above the city. Up from the cobbles of the central streets still rise the sculpted grey boulders - up to five metres high - of Inca walls, monumental and delicate at the same time, becoming larger as they approach the towering Spanish adobe behind which Pizarro´s lucky sergeants and corporals lived with their Inca-princess views. Out in the wide green valley that holds the city, Inca irrigation systems still water the little fields. Around the skyline I could see the notches at the four points of the compass where the paved imperial roads led away to the far quarters of the empires: the Pacific, Colombia, Argentina, the rainforest.

Cusco goes on changing. It is the only place in the Americas you are ever likely to see a cinema shoehorned into pre-Columbian architecture - although the cinema has just closed, because Cusqueños have switched to watching DVDs instead. The city roughly tripled in size during the 1980s and 1990s as campesinos fled from the war with the Shining Path rebels, so self-built shanties spread up every hillside now. In the center a new colony of affluent Europeans and North Americans is settling in among the backpacker bars, attracted by the property prices and by an increasingly sophisticated restaurant scene. But what makes visitors stay is precisely the living presence of the city's past in its atmosphere today. Inca stones, Spanish arches, wooden balconies overhanging streets just wide enough for one tiddly Suzuki taxi at a time: in Cusco the centuries since the conquest feel close by, and the imagination can reach out easily to the time before it, when plaza was surfaced for the emperor's pleasure with white Pacific sand imported on llamas, and the sand was seeded with tiny gold and coral creatures representing all the provinces.

For one thing, the people of the empire were going about their business all around me. The black-haired, long-nosed, almond-eyed street children trying to shine my shoes were the heirs of the city's builders; and so were the ladies with the stovepipe panama hats trying to sell me a jumper with marching llamas on it; and so were the families going out for roast-pork treat at the Formica tables of a chicharonneria . They spoke Quechua, the language of the empire. They practised the folk medecine of the empire, rubbing their heads with rue if they came home with a headache, burning the rue so the ache went up in smoke with the herb. ´If that fails, then you try an aspirin, ´ I was told. Everywhere there were fragments of the past, everywhere there were teasing mixtures of the old and the new. The Quechua of Cusco are passionate Catholics now, but the local painters who were set to work in the 17 th century turning doctrine into vivid pictures faced a few challenges, like the problem of portraying sacramental bread to a culture that didn't grow wheat. Bread had to be replaced, at first, by a food just as symbolically powerful for the Quechua. Which is why in the cathedral, crowded with so many gilt-edged imagines that walking up its aisle is like stepping though the pages of a giant baroque comic book, you eventually find a Last Supper where Christ and his discipline are sitting down to side dishes of maize, banana and chilli - and a main course of crispy, roasted guinea pig. It looks just the same as it does in a Peruvian guinea-pig rotisserie today, with its little legs splayed out pathetically on the plate.

I was staying at the Hotel Monasterio, where the Orient-Express Hotels group has turned a former Jesuit cloister into an experience of theatrical splendour. The galleries around the courtyard have been glassed in, carpeted and hung with religious art. The stonework has been buffed to a high shine. Fountains play and oxygen puffs down discreet pipes into favoured bedrooms. Orient-Express also operates the only hotel permitted at the site of Machu Picchu, the Sanctuary Lodge, and, in the past few years, has expanded its empire to take in the railway between. At 8:30am on the day I was scheduled to go to Machu Picchu, I was standing on a platform in the outskirts of Cusco with a Champagne flute in my hand, as blue and gold carriages slid to a halt in front of me.

To the sensibly comfortable services on offer, Orient-Express has just added an option that goes well beyond sensible, in the form of a luxury train named after the Ivy League explorer who discovered Machu Picchu in the 1910s. The Hiram Bingham is three carriages of satiny tropical hotel chic on wheels. Its tablecloths were snowy. Its version of the Pisco sour was the best I tasted in Peru - which is saying quite something as everybody in the country seems to have an active opinion about how to combine the egg white, bitters and grape liqueur of the national cocktail. Los Hermanos Vera, a duo of brothers famous in Cusco, were serenading in the bar. It is the only train I have ever been on where Molton Brown Soothing Hand Lotion is on tap in the lavatories.

But as we moved off along the narrow-gauge track, down a gentle valley of red earth and eucalyptus trees, pasta markets selling armfuls of the green barley Peruvians feed to their guinea pigs, something seemed familiar. The valley narrowed, became stonier: I got it, I was remembering childhood holidays when I pestered my parents into taking me to the Ffestiniog Railway in Wales, so I could gaze at slate hillsides and breathe in the steam-engine perfume of hot tar and oily water. This, too, was am industrial railway built to carry heavy commodities from awkward places, in this case the slides of beef and sacks of coffee from lowland ranches beyond the mountains. This, too, clung to the walls of rocky gorges, and squealed metal against metal as it went around tight corners. It is only an accident that it passed the site where Bingham stripped back the undergrowth to reveal wonders. Thoomb-boomb, thoomb-boom, thoomb-boom, thoomb-boom, said the wheels, and down to Machu Picchu we went, at a stately 15 miles per hour.

The panorama beyond the glass grew more and more spectacular as we descended from ecology to ecology, from step to step on the great staircase of altitude. Through a cranny in rocks green with copper deposits we crept out into the ´Sacred Valley´ of the Urubamba River, a swift muddy stream flowing between high valley walls tattooed from top to bottom by the Incas with terracing; then alongside the river as it wound round the roots of taller and taller monoliths of Andean granite, until the sky was only a cloudy slot far above, and the mountains had turned into rearing obelisks as strange to the eye as the stylized peaks in Chinese brush paintings. Meanwhile, the harsh lichen-green of the slopes further up had turned to a mossy emerald, then to a wet undergrowth bursting with flowers, then to cloudforest tree hung with creepers and colonized by bromeliads. By now the backpacker-beloved Inca Trail had started up on the opposite bank, and occasional flashed of orange Gore-Tex through the foliage showed where someone was tramping to Machu Picchu on the ancient stones of the royal road. By now, the waiters on the Hiram Bingham had started to serve an appetizer of roasted alpaca with julienned cape gooseberries. In the brief dark of tunnels, lamplight reflections of napkins and silverware replaced the Andes.

The station for Machu Picchu is Aguas Calientes, a tourist town threaded along the valley floor. The rails run straight down a street of shops selling pizza and ponchos. From there, a bus ride regained about 500 metres of the 1,500 metres I'd just descended in the train. The road climbed the mountainside in a dizzy succession of switchbacks, with a wider and more jaw-dropping vista at each corner. A cluster of giant granite teeth crowded close together, tropical green from base to crown. Machu Picchu, terminus of the Inca Trail, lost city of the emperors, was perched in the sky on the saddle between the two peaks of one tooth, surrounded by sheer cliffs. Or it might be more accurate to say that it was sculpted into the saddle, because the contours of the top of the mountain had been bodily remade for the sake of this exercise in imperial astonishment. The grey stone beneath the lush leaves had been forced into curves for terraces; ground into angles for ramparts on the brink of the drop; carved into strange polygonal pieces for buildings; engraved on the grand scale. The Inca Empire had no coinage. The emperors took their taxes in labour, and on this insanely placed dwelling in the clouds, they had spent work like water.   Effort made granite soft, made it yield to the store of shapes in the human mind. Rosa de piedra , Neruda called it: pan de piedra, luz de piedra, vapor de piedra, libro de piedra :´Rose of stone, bread of stone, lamp of stone, gas of stone, book of stone´.

Machu Picchu is a peaceful, however many visitors file through its arches and along its passages every day. The Spanish never found it. It was never sacked, never burned. It was quietly abandoned, and the thatch rotted away from the grey-stone gables. Yet it's here you realize that all the communities between the country's past and the present can't reverse the central consequence of the conquistadores´ vandalism. The Incas didn't use writing, so when the way they lived was smashed to smithereens, no record remained of what they'd meant by anything they did. The broken pieces reused in the new mosaic became cryptic. And where therem were no people any more, as at Machu Picchu, the mystery became complete. The thing survives, but not the intention behind it. There are only the better and the worse guesses of generations of archeologists. Was this a temple? Is that a dormitory? Was Machu Picchu a barracks, a university, a place of pilgrimage, or an imperial cottage in the country? Who lived here? Vestal virgins, hostages, high priests, princes in disgrace? No one knows, Machu Picchu is mute. Every morning at dawn fingers of white clouds reach up from the valleys and rinse the ruins clean. Every day, they start again blank. I picked a purple orchid and pressed it between the pages of my notebook.

SCALING THE HEIGHTS

Peru is a big country. Anyone intending to visit more than one of its very different regions - to do justice to the pre-Inca cities of the northern coast, for example, or to explore the jungles of the Peruvian Amazon - will need weeks rather days. But there is a compact circuit in the south that offers dramatic contrasting experiences in a manageable space of time.

Once ice-cold river, a green thread through high desert, keeps alive city of Arequipa , a haughty provincial capital with an old centre built of white volcanic stones. The mountains they came from ring the city, exhaling faint steam against brilliant blue skies.

Equally brilliant are the painted adobe walls of the Santa Catalina Monastery , once a miniature town in itself at the city's heart. Visitors can step beyond the barred screens of the entrance parlour into cloisters ornamented with frescoes of birds and Bible scenes. The mestizo-baroque carvings wriggling over the front of the Jesuit church of La Compañia entangle Catholic and Andean motifs, so that European cherubs in ruffs mix with pumas, serpents and feathers. The famous child-mummy, Juanita, a girl who was sacrificed on a mountain-top in the 15 th century, is on display, crouched eerily in a freezer, at the Museum of Andean Shrines .

You can shop for alpaca knitwear in the former monastery behind La Compañia; if money is really no object, this is the place to buy a coat or a scarf woven from the 100g or so of super-fine wool that vicuñas yield each year.

From Arequipa, you can drive up and over the breathless Pata Pampa pass to the Colca Canyon , a dramatic gash of fertile green in the crumpled red moonscape of the highlands. Along this isolated valley, over 3.000 metres deep, the contour-hugging crop terraces of a pre-Inca culture are still being ploughed by oxen behind twisting stone walls. Giant hummingbirds feed from cactus flowers, and if you're   lucky   you can see condors riding the thermals between the rock walls. The Orient-Express Hotels group owns a lodge in the valley, the Parador del Colca (doubles from about £45), an ecofriendly building with hotwater bottles and stone hearths. Book through the Miraflores Park Hotel in Lima (00 51 1 610 4000; www.mira-park .com).

Cusco is the centre from which to explore the Inca heartland, and is itself a treasure house, with the monolithic, inscrutable grandeur of Sacsayhuaman above the city and the telling paintings in the Museum of Religious Art. The city is also the centre of New Andean Cuisine , a delicious   experiment with local ingredients, largely aimed at the palate and wallet of travellers. Try the quinoa gnocchi at Cicciolina (Calle Triunfo 393; 00 51 84 239510; about £10 for two without wine), the Spanish-Quechua-Japanese-French fusion food at the Inka Grill (Portal de Panes 115; 00 51 84 262992; dinner about £14 for two without wine), and the Map Café in the Museum of Pre-Columbian Art (plaza de Las Nazarenas 231; 00 51 84 242476; about £34 for two without wine).

Along the valleys   to east and west of Cusco, pay a call on the mysterious Inca site at Tipón , where stones channels of running water make   geometrical patterns   on clover-dotted turf, and at Pisac , where a red granite temple poised on a mountain shoulder looks down on a spectacular sweep of the Andes. The place to stay in Cusco in the Hotel Monasterio (00 51 84 241777; www.orient-express.com; doubles from £191).

Machu Picchu needs no recommendation. Unless you walk the Inca or other trails, it is reachable only by train and bus, in which casa consider taking the Hiram Bingham (£272 return per person, including brunch, tea, cocktails and dinner, bus transfers and guided tour).

There are less indulgent hotels in Aguas Calientes below the site, but if you stay at the Sanctuary Lodge (00 51 84 211039; www.orient-express.com ; doubles from about £323), you get extra hours of daylight at the site, an easy opportunity to visit it at dawn as the tropical mists boil over it, and a convenient spot to rest your legs after taking the walk up and down the terrifying rock spire of Huayna Picchu , just beyond the Inca city. A word   of caution: the final ascent to the pinnacle at the top requires a scramble through a tight and muddy tunnel, but the view repays it.

Finally , Lima , the only gateway for international flights, is an inevitable part of any Peruvian journey.

The capital is no longer the New World jewel it once was. But the museums and colonial churches of the   central   district are still worth a visit, and the prosperous suburbs of Miraflores and San Isidro provide a secure base. For a rare glimpse of Lima society over the last century, make an appointment to visit the Art Deco mansion casa Garcia Alvarado in Miraflores (book through Aracari, see below).

For sublime seafood, try the extremely fashionable Los Pescados Capitales (avenida La Mar 1337, Miraflores; 00 51 1 4218808; about £17 for two without wine; lunch only); the name translates roughly as ´The Seven deadly Fins´.

GETTING THERE

British Airways (0870 850 9850; www.britishairways.com) flies from Heathrow to Lima via Madrid or Miami (onward legs operated by Iberia and American Airlines) from about £900 return in October. KLM (0870 5074074; www.klm.com ) flies from Heathrow to Lima via Amsterdam from £637 return in October. Iberia (0870 609 0500; www.iberiaairlines.co.uk ) flies from Heathrow to Lima via Madrid from £650 return October. The author's trip was organized by Lima-based Aracari Travel Consulting (00 511 242 6673; www.aracari.com ). UK tour operators offering trips to Peru include Elegant Resorts (01244 897000); www.elegantresorts.co.uk ). Cazenove+Loyd (020 7384 2332; www.cazloyd.com ). Last Frontiers (01296 653000; www.lastfrontiers.com) and Discovery Initiatives (01285 643333; www.discoveryinitiatives.co.uk )

TRAILBLAZING

After three decades as the must-do trek in South America, the Inca Trail is in a perilous state , with conservationist warning that the famous city could slide off its mountain saddle. In June, UNESCO even considered adding the site to its List World Heritage Sites in Danger.

As a result, the Unidad de Gestion Machu Picchu, the Peruvian body that oversees conservation on the trail, recently set a limit of just 500 walkers per day on the trail, charging US$50 per person.

As this figure includes al porters, cooks and registered local guides, tour operators are urging those intent on walking the trail the book at least three months ahead, if not six , particularly for travel in the high-season months of July and August (try to go in May-June or September-October if you can). To be sure of securing permits, agents have to make block booking well in advance, providing the names and passport numbers of every individual concerned.

There are other ways of visiting the site: by staying in sanctuary Lodge or taking a train and bus (see Scaling the heights).

Francis Spufford