Between 5,000 and 13,000 people were executed at Sednaya in the four years after a popular uprising descended into war, it said.
Amnesty International called for the end of these extrajudicial executions and the inhumane treatment of prisoners at all government-run prisoners in Syria.
At regular intervals, the Amnesty report said, they are gathered in the middle of the night from their cells and taken blindfolded to an execution room on the grounds of the prison near Damascus, where they are hanged. Amnesty International characterized the killings as an "extermination" of political dissidents that has been authorized by the highest levels of the Syrian government.
Syrian government officials rarely comment on allegations of torture and mass killings. In the past, officials have denied reports of massacres documented by worldwide human rights groups, denouncing them as propaganda.
Mr Alshogre survived nine months in the prison, paying his way out in 2015 - a common practice. "The UN must immediately carry out an independent investigation into the crimes being committed at Saydnaya and demand access for independent monitors to all places of detention", she said. "What is important is that there needs to be accountability for all the victims in this conflict".
But the Amnesty International report says the magnitude and severity of abuse has "increased drastically" since 2011.
"The families of the tens of thousands of prisoners who have been forcibly disappeared, tortured and killed in the custody of the Syrian authorities have a right to know the fate of their loved ones", the report concludes. For the young ones, their weight wouldn't kill them.
During its research, Amnesty spoke with survivors of Saydnaya who produced firsthand testimony of a world inside the prison that is "carefully created to humiliate, degrade, sicken, starve and ultimately kill those trapped inside".
Amid compelling evidence that the Syrian president's henchmen carried out an unprecedented "policy of extermination", the Foreign Secretary said the dictator had "no future as leader".
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The chilling accounts in the Amnesty report came from interviews with 31 former detainees and more than 50 other officials and experts, including former guards and judges.
"For many prisoners, [Saydnaya] will be the the last place they will ever be sent because they will die at the prison", report author Nicolette Waldman tells The Current's guest host Laura Lynch.
"They walked in the "train" so they had their heads down and were trying to catch the shirt of the person in front of them. Actually, they were supporting al-Nusra (al-Qaeda in Syria) and ISIS from the very beginning, they were extremists from the very beginning, so they can not destroy and build at the same time". "I'm just a headline-the bad president the bad guy, who is killing the good guys", Assad told the New York Times. "It sounded like they were skinning them alive", former detainee Nader told Amnesty International.
COMBO - In this combination of two photos of Omar Alshogre, a 21-year Syrian former detainee, now living in Stockholm, Sweden.
But later, "there would be this unusual silence", broken only by the sounds of truck engines, Shogre said.
The bodies of those killed were allegedly then loaded onto lorries, and transferred to Tishreen military hospital in Damascus for registration and burial in mass graves located on military land. However, the figure does not include those hanged at Saydnaya. One of his cousins died in his arms because he was so deprived of food, while another of his cellmates died of diarrhoea - a common occurrence inside the prison.
Still, Mr Alshogre said nothing could have prepared him for Saydnaya. "Moreover, reports from one organization citing anonymous sources are not enough", he said. I remember the guard would ask how many we had.
Waldman says their treatment at Saydnaya is "almost hard to comprehend".