They represent the work of some of the nation's finest craftsmen. Yet the church buildings of Scotland, which number roughly 3500 across the country, are under threat as never before.

According to the Scottish Civic Trust, which advises the government on conservation, some 300 of these are on their at-risk register: buildings that are falling into serious disrepair because they are not in use.

Scotland does have a particular problem because of the history of disruption and schism in the Church of Scotland in the nineteenth century. Since the 1920s, the Kirk has been seeking to get rid of what is described as an over- provision of church buildings, often by merging congregations.

One of the most high-profile churches earmarked for closure is Govan Old Parish Church in Glasgow. Its parishioners, along with those of Linthouse St Kenneth's Church, will now attend services at the nearby New Govan Church. The decision has been met with disbelief because the site has had a religious presence since the sixth century and is known for its collection of 31 pre-Christian and Christian sculptured stones which date from the ninth century. The present A-listed building, which was completed in 1888, was designed by Scottish architect Robert Rowand Anderson. It boasts stained-glass windows by Charles Kempe and a monolithic sarcophocus - the only one in Scotland.

A daily service has been held there since the building opened, and generations have worshipped there. Robert Preston has been going to services there for 67 years. "I was born in Govan and I was Christened in this church," he says. "My granny was a member and the family even have their own pew. When I heard the news I thought it was a cut-up: the decision had been made before it came to us. It's a sad day.

"We've known for a wee while that the three churches were coming together but we never thought it would be this one which closed. I just don't want to attend any other church so I'm not going to church at all and I've been forced into that by the Church of Scotland. I feel very strongly about this church - we need to keep it."

The Rev Dr Norman Shanks, the current minister, retires at the end of this month. He hopes that the building can still be used as a focal point for the community. "The congregation is not as big as it used to be but it still is very active and committed and engaged with the life of the community," he said. "A lot of people have expressed surprise and I think the people of Govan Old were disappointed. There is a mixture of emotions going around but they now have to look to the future and they are being very gracious, resilient and positive."

Beyond the concerns of the immediate congregation, the announcement has been greeted with dismay in the area's wider community. Pat Cassidy, managing director of Govan Workspace, has spent the last three years putting together a conservation plan for Govan that envisions Govan Old Parish Church as having a major role to play in the future of the area. "We've just completed an architectural study which shows how the Old Govan Parish Church can act as a catalyst for the regeneration of the area; the church was critical to that redevelopment plan. It is as important as Iona and we believe that its future is absolutely critical to the regeneration of that area of Govan."

Cassidy believes that any change to the function of the church must be sympathetic to its traditional role as a place of worship. "The fact that it's the oldest known Christian settlement on the Clyde means it would be a tragedy if it was turned into a pub," he says. "It would be like turning the Cathedral at Iona into a furniture centre: it would be absurd. We think the decision is short-sighted and lacks vision.

"We are absolutely convinced that a major regeneration of that area will take place and when it does the church would have such a high profile that it could be one of the most important tourist destinations in Glasgow. Steps are going to have to be taken to ensure that it retains a dignified status and it has to continue to have some kind of ecclesiastical function because of its illustrious history."

Scottish Redundant Churches Trust seeks to preserve churches as historical buildings with provision for occasional religious ceremonies. The charitable trust was established in 1996 to preserve churches of exceptional architectural and historic importance that no longer have a congregation. It now has five in its care.

Victoria Collison-Owen, the trust's executive director, says: "We fully recognise that there are too many churches at present in Scotland because of historical events, and therefore some rationalisation is needed. We want to see re-use of church buildings that is entirely appropriate for each individual building. We are not against conversion and re-use of places of worship as such, but we do firmly believe that there are some buildings which are of such exceptional quality, and which are part of our heritage, that to alter them radically would result in a loss of that heritage."

East Cromarty Church on the Black Isle has been in the care of the trust since 1998. The main parts of the building which still stand today date from the eighteenth century, although some parts date from medieval times. The graveyard includes gravestones carved by pioneering geologist and writer Hugh Miller. After it appeared on the BBC programme Restoration Village in 2006, the church's profile enjoyed a significant boost and visitor numbers surged as a consequence. Last month the church was granted £641,000 from the Heritage Lottery Fund and it is hoped that it will become a venue for concerts and weddings as well as a place of worship.

Jean Newell, a 98-year-old parishioner who has attended services in East Cromarty Church since she was five years old, was involved in the Restoration Village campaign. "My father was the beadle of the church and I was always there to help him," she says. "In those days everybody went to church - it was packed. Cromarty itself is a different place altogether now. I think it will always be an important building but, of course, in a changing world. What I feel is important young people don't necessary feel is important, but I'm hoping that when the place is completely renovated that it could be used for lectures because the acoustics are good."

Collison-Owen agrees that shrinking congregations mean more churches will face the same dilemma. "Falling numbers is a significant factor but we are aware that everything changes," she says. "Sometimes closures of church buildings are very short-sighted and perhaps it would be better to look to the future and what is likely to happen in the community. Will there be a new minister? Will there be new housing built? I think there is an argument for mothballing certain churches and saying that we don't know know what will happen in the future, but we may wish to re-start worship here on a regular basis in times to come.

"We do see the continuation of worship in the churches in our ownership as very important indeed. To close a church and cut off that continuity is very sad so we allow the church to be used occasionally for religious purposes but also to open up the use of the building for other appropriate secular uses. A lot of the churches which close are in rural areas, when the area has lost its shops and its post office, the pub and school - all the public gathering places have gone, and the church can be the one thing that's left."

In Scotland's cities, churches have been transformed into bars, restaurants and theatres with much success. Oran Mor and Cottiers in the West End of Glasgow and Bedlam Theatre in Edinburgh are some of the best-known examples. Steve Irvine, formerly a seaman in the Royal Navy, set up a climbing centre in the Old St Andrew's Church in Leith in 1994.

The centre, called Alien Rock, now has around 50,000 visits a year and the huge space incorporates a seating gallery, shop and a reception area. "We weren't looking specifically for a church building but churches tend to have the required height," says Irvine. "When we came across this building it was disused but it had been a fitness centre and before that a judo centre."

A three-month renovation involved removing seating galleries on the first floor and fitting extensive steelwork to create the climbing walls. "The response from the community has been very good," says Irvine. "People come in and say, Oh, I remember when we were married here'. Long before we moved in, the church moved the congregation round the corner to another church, which unfortunately has also gone - it's been developed into flats.

"I think people are just happy to see St Andrew's still in use."

In April, the Scottish Civic Trust published a report with included 101 Uses for a Redundant Church which listed current uses for former religious buildings. Here are some of the more quirky examples:

Sheep Shed, St Margaret's Kirk, Orkney.

Wool is big business in Sandness, where the island's only wool spinning mill is located. When the Kirk fell into disuse, it was only natural for the town's lucrative four-legged population to take up residence there.

The building is located west of Sandness and is surrounded by a large graveyard.


Sikh Temple, St Thomas's in Sheriff Brae, South Leith.
The church was built between 1840-43 by architect John Henderson for Sir John Gladstone of Fasque, born in Leith and father of prime minister William Gladstone, as a memorial to his family. When the congregation united with the Junction Road Church in 1975, the building became available. In 1976 it opened as a Sikh temple. It was the target of a fire attack in 1989 but the community rallied round and it quickly re-opened with a multi-cultural service.

Casino, St George's Chapel, Edinburgh.
The chapel is located on the south side of Queen Street, close to the National Portrait Gallery. It was erected in 1794 from designs by the Scottish neoclassical architect Robert Adam. After it ceased to be a place of worship it was a showroom for bathroom equipment. In 2002 it re-opened in its current un-Godly incarnation as a casino.

Backpackers' Hostel, Belford Church, Edinburgh.
Travellers to Scotland's capital can now spend a night under the roof of this nineteenth-century Gothic-style church which still boasts stained-glass windows - something to tell the folks back home. The congregation united with the Palmerston Place Church in 1970.

Cinema and Theatre, Anderson Free Church, Glasgow.
Anderson Free Church was designed by James Sellars and built in 1877. In the 1950s, it came under the ownership of Glasgow University. It was renovated in 1997 with money from the Scottish Arts Council National Lottery Fund and is now a film and theatre venue and base for the University's film and TV department.