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Twenty-three of the bodies were found in a concealed chamber beneath a remote farmhouse in the village of Cheiry, 48 miles north-east of Geneva.
A further 25 bodies, including some children, were recovered in three burnt-out chalets in Granges-sur-Salvan, 47 miles east of Geneva, near the Italian border.
The deaths have been linked to the apocalyptical Order of the Solar Temple sect, which was founded in 1984 by Dr Luc Jouret and Joseph di Mambro.
The Order of the Solar Temple condones the mass stock-piling of weapons to prepare for the end of the world.
Just hours before the grisly discoveries in Switzerland, the bodies of two more people, also believed to be linked to the sect, were found in Quebec, Canada, in a burnt-out apartment owned by Dr Jouret.
It is not known yet whether either of the cult leaders are among the dead, but the Swiss authorities have said they are searching for two people in connection with the deaths.
In Cheiry, emergency services were called to the farmhouse after locals reported a fire.
Initially they only discovered the body of the farm's owner, 73-year-old Alberto Giacobino, who was lying dead on a bed with a plastic bag over his head. He had also been shot.
The concealed chamber, covered in mirrors, was discovered during a search of the property for further bodies.
Many of the bodies were found with gunshot wounds and plastic bags over their heads. Others were found clasping their hands in prayer. Most of the bodies were clad in ceremonial robes.
According to rescuers, champagne bottles littered the floor and the victims were lying in a star formation.
On a make-shift altar within the chamber there was a rose, a cross and a picture of Mr Jouret. The sect's motto is "Rose Eternal Cross."
Plastic bags of petrol and gas cylinders wired up to explode by a telephone signal were found although the system had failed to work. It is thought a second fire was started manually elsewhere in the building.
A similar timer device had also been rigged up in Granges-sur-Salvan. However, it is thought the dead may have been drugged or poisoned before the fires began.
Local people in both idyllic villages had no idea that cult members had been living in their midst and have been left shocked by the events of the past 24 hours.
Similarities are being made to events in Jonestown in Guyana in 1978 when 914 people led by the Reverend Jim Jones, committed suicide in a jungle clearing.
And just last year in Waco, Texas 80 members of the Branch Davidian sect, led by David Koresh, died after fire broke out during a siege.
It was revealed following the mass suicides that the Order of the Solar Temple sect owned extensive property in Switzerland, Canada and France and was heavily involved in money laundering and arms trafficking.
International arrest warrants were issued for Luc Jouret and Joseph di Mambro who were suspected of mass murder, but their bodies were eventually discovered among the dead in Switzerland.
Two days after the Swiss suicides the bodies of Antonio and Nikki Dutoit and their three-month old son, Christopher, were found murdered in their home at Morin Heights, Quebec. The couple had left the Order of the Solar Temple sect three years previously but possibly "knew too much."
In December 1995 16 members of the sect were found dead in France and in March 1997 five more died in Quebec.
In 2001, Michel Tabachnik, a former conductor with the Canadian Opera Company, was cleared of contributing to the 74 deaths of the members of the Order of the Solar Temple between 1994 and 1997.
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