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Most of the 88 detainees killed were found to have been tortured or ill-treated.
Amnesty International has accused Syria of "systematic persecution on a vast scale" in a report that says at least 88 people have died in detention in since the anti-regime uprising began in March.
The group said that 10 children were among those killed – and that the majority of the victims had been tortured or ill-treated.
Injuries ranged from burns, whipping marks, electric shock marks, slashes skin and mutilated genitals.
Amnesty said it believed that all of the dead had been arrested after participating in anti-government protests.
The victims' names were documented by the group, along with the dates and places of arrest. The Guardian reported that independent forensic pathologists established the possible causes of death "in some cases by examining film of the bodies".
Neil Sammonds, Amnesty's researcher on Syria, told the BBC the deaths of Syrians in custody were reaching “massive proportions”.
He said Amnesty had the names of at least 3,000 people currently being detained.
There are said to be 12-15,000 people detained in the country at the moment. We know that torture has been widespread over many years and it has got much much worse. Most people are held in incommunicado detention.
Amnesty's allegations come as activists reported widespread anti-regime protests across Syria on Tuesday — the first day of the Eid al-Fitr feast that marks the end of Ramadan.
At least seven people were reportedly shot dead when security forces opened fire on protesters.
The Local Coordination Committees activist network said that most of those killed were in the south, near Deraa, where a "huge" protest was formed as worshippers emerged from the al-Omari mosque.
(GlobalPost in photos: Syrian protesters and their supporters)
The U.N. has previously said that Assad's regime could be guilty of crimes against humanity.
It estimates that more than 2,200 people have been killed in the government's crackdown on protests.