The organization said its researchers found evidence of at least 27 facilities across the country where tens of thousands of people have faced government-sanctioned abuse.
Former detainees and defectors identified the locations of the centres, the methods of torture, and the agencies responsible. The rights organization released sketches by a Syrian artist depicting the abuse.
“The intelligence agencies are running an archipelago of torture centres scattered across the country,” said Ole Solvang, emergencies researcher at Human Rights Watch. “By publishing their locations, describing the torture methods, and identifying those in charge we are putting those responsible on notice that they will have to answer for these horrific crimes.”
Human Rights Watch said its 81-page report is based on more than 200 interviews with former detainees and defectors conducted since March 2011, when anti-government protests began.
A young man named Wael said Syrian intelligence officers beat him after he was detained in the central Syrian city of Homs.
"When we were detained in the Homs Military Intelligence Prison they hung us by our arms with our bodies suspended in the air," he said.
"They beat us and said, 'You want freedom? You want democracy? Here is your freedom. Here is your democracy'."
Others said they were subjected to mock executions and sexually assaulted.
A 13-year-old former detainee said interrogators jolted him with electrical currents until he passed out and pulled out his fingernails.
Some described enduring "dulab," in which torturers force the prisoner's legs and head into a car tire before beating them.
"People have definitely died as a result of the torture," said David Mepham with Human Rights Watch in London.
The organization said Syrian President Bashar al-Assad and some of his officials should be tried for crimes against humanity before the International Criminal Court and has asked the UN Security Council to refer the cases to the ICC.
"The systematic patterns of ill-treatment and torture that Human Rights Watch documented clearly point to a state policy of torture and ill-treatment and therefore constitute a crime against humanity," the group said.
"We hope that the material we provide will further galvanize international action to really put pressure to bear on the Syrians — and that particularly means Russia and China that have blocked action against the Assad government," it said.