Demonstrators protest against Syria's President Bashar al-Assad after Friday prayers in Yabroud, near Damascus, June 29, 2012. Human Rights Watch has documented Syrian men, women and children being arrested, tortured and forced to confess to taking part in protests
The organisation says it has interviewed more than 200 former detainees and identified at least 27 detention centres across Syria.
Its details horrific torture methods, enforced disappearances and arbitrary arrests.
The report claims the regime's actions amount to a crime against humanity.
Human Rights Watch wants the regime to be tried at the International Criminal Court (ICC), but correspondents say any such move is likely to be blocked by Russia.
UK Foreign Secretary William Hague said the report "should act as a clear warning".
"Those responsible for systematic and widespread human rights violations should not delude themselves: we and our international partners will do everything we can to ensure that they will face justice," he said.
The report, "Torture Archipelago", draws on the testimony of more than 200 former detainees, including women and children, to describe what it says are cases of mistreatment and torture since March 2011.
Human Rights Watch said everyone it interviewed described conditions of extreme overcrowding and a lack of food, while many said they had been forced to sign or fingerprint confessions admitting that they had attended anti-government protests.
The majority of the eyewitnesses also said they had been tortured and several of them claimed to have seen people die from torture in detention.