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Ladakh is a high-altitude desert, desiccated and stark, and its capital is at 10,500ft (3,200m). Altitude does funny things, and some not so funny. For a start it pressurises your sun cream tubes so that when you unscrew the top your factor 15 makes a run for it, in an unremitting, long, white worm. Some people suffer headaches and nausea, but they won't know until they get there; mountain sickness is unpredictable.

In Ladakh there is even less oxygen because at this altitude there is so little vegetation. Which is why, having climbed 21 steps to the first floor of the house I was staying in, slightly breathless, heart pattering, I took the locals' advice and did nothing else that day except acclimatise. That meant reading, drinking a lot of water and eating – porridge, toast and curried scrambled eggs for breakfast; salad and tuna fishcakes for lunch; spinach soup, chicken curry and banoffee pie for supper. The terrain may be rough; the living is not.

You stay in village homes, but in the comfort and style of a country hotel rather than a peasant farmhouse. It's an idea that Shakti Tours, an imaginative Delhi-based agency, established in two other parts of the Himalayas – Kumaon and Sikkim – and has now brought to Ladakh.

The rewards are great. You get to parts of the country only seen previously by backpackers, and are privy to a way of life that can come only from living among the villagers.

In Ladakh, the upper floors of houses in three villages have been transformed with marble shower rooms, Tibetan carpets, pastel colours, parquet floors, and sometimes wayward plumbing. Sticks of juniper, brought from Sikkim, smouldered as incense. Call it Himalayan chic.

The house I stayed in in Stok, a village half an hour from Leh, was a substantial, four-square building, which had little turrets at its corners and heavy frames around its windows in dark wood, like kohl. It reminded me of an Edwardian seaside villa. It was built with mud bricks for insulation, and from the outside only one thing distinguished it from its neighbours: instead of parapets of drying cow dung, which would be burned as fuel, there was a cotton awning on its roof, sheltering a couple of day beds. That, and the fact that there were no cows living on the ground floor. As in the Alps, cattle supplement the houses' winter heating. Here we had people. A family of 11 lived discreetly downstairs.

Dinner was in the farmhouse kitchen, a large, low-ceilinged room with a wooden floor. Candles flickered shadows across four timber pillars and the stout beams they supported. It was like eating in the wardroom of a ship in Nelson's navy, an effect heightened by windows with small, Georgian panes. Against one wall, on shelves above the traditional range, were countless pots in aluminium and beaten copper.

The house is on the edge of the village, looking up a valley to the 20,079ft (6,120m) peak of Stok Kangri. Small fields, enclosed by stone walls, contained tethered cows and white Buddhist stupas – mounds containing religious relics – plus wheat, barley and magpies. There are also apricot orchards and spinneys of willow and poplar – lowland trees, incongruous in Himalayan highlands.

It was late September. When the sun came out it was hot; when it went in, and the wind rose in the afternoon, it was bitterly cold. There were a few granules of snow. After Siberia, Ladakh is the coldest inhabited place on Earth. Men came to light the Bukhari wood-burning stove, a steel box on little cabriole legs. Within minutes the room was verging on hot. At night a "hot water bag" was slipped under the duvet.

Stok, population about 260, is a scatter of houses and small fields on the gentle western slope of the Indus valley. From Leh, you pass the prison with eight inmates, go around a stupa, where traffic is diverted clockwise in deference to Buddhist protocol, and cross the river via a steel bridge wrapped in red and blue prayer flags of faded cotton. In Buddhism, faded is good: it shows the prayers are being properly dispersed by the sun, wind and rain.

We walked through the mountains, picnicked in orchards and rafted on the Zanskar river in a gorge of plumcoloured rock. I watched men moulding mud bricks, women winnowing barley and a tinsmith working at a forge blown by sheepskin bellows. In one village I awoke to a woman making chapatis below my bedroom window. Her hotplate was a slate, balanced on stones over the fire.

In the village of Nimoo I met Dashi Norboo, a man of many titles. He is the village headman, or goba, who has also earned the affectionate sobriquet of abalay, or esteemed father. But his most important role is that of churpun, head of water. Dressed in a snappy straw trilby and auburn robe, he showed me the elaborate network of stone channels from which the village draws its supply. The system, as much as 800 years old, ensures every part of the village gets at least four hours' water a day. On Sundays and Wednesdays clothes may be washed. There is a "heavy fine" of 500 rupees – about £7 – for transgressors.

Water is precious in Ladakh. So is religion. Only Tibet has a greater concentration of Buddhist monasteries. Ladakh is known as Little Tibet. Thikse gompa, or monastery, built in the 15th century, is like a small hill village with white buildings spilling down the side of a rocky knoll. The sacred parts – the prayer halls, frescoes and a 50-feet-tall figure of the Buddha – are at the top. When I arrived at dawn, as the shadows were sliding from the hillsides, two lamas appeared on a roof terrace. They wore maroon robes and yellow woollen helmets, shaped somewhere between cockscombs and tea cosies.

Hats are the emblems of an ancient schism. Centuries ago the monks all wore red hats but, at one ceremony, the stock ran out. The next monk in line grabbed the nearest alternative, which happened to be yellow. Thus did Ladakh's two sects – the reformist yellow hats and conservative red hats – come into being.

From their balcony high above the Indus valley, the lamas sounded conch shell trumpets to announce the start of morning devotions. Thikse was the first monastery to admit outsiders to its prayers. It is a rococo ritual of incense, chants and porridge.

In a red and gold pillared hall, dimly lit by bare bulbs, monks sat cross-legged at lines of low benches laden with thick texts. Boy monks chirruped to keep up as the adults rattled through their mantras. Incense drifted through light beaming from the doors. Every so often the chanting was interrupted by sudden explosions of noise – tinkling bells, blaring horns, crashing cymbals and drums.

And all the while the smallest monks – boys of six and seven – scampered about, collecting pails of barley meal and outsized aluminium kettles of butter milk, almost as big as themselves. They lugged them along the benches and poured their contents into bowls. During lulls in the chanting the monks tucked in. It was a scene at once mundane and mystical, homely and exotic – like this holiday, a privileged glimpse of Ladakh itself.