In the jails and interrogation centres of secret police, prisoners have been brutalised, either at the hands of officers, or more often with a bottle or other utensil.
"In detention facilities rape is clearly used as a form of torture to humiliate and degrade people, and to bring back the wall of fear," said Nadim Khoury, Deputy Director for the Middle East at Human Rights Watch.
The claims come as Britain prepares to launch a campaign against rape as a weapon of war that will be the centrepiece of its presidency of the G8 countries next year.
William Hague, the Foreign Secretary, will today recruit the Hollywood actress Angelina Jolie to highlight the issue at a meeting at the Foreign Office.
He has ordered the establishment of a special diplomatic team to document and help ensure the prosecution of sexual war crimes in conflict zones to support the initiative.
Meanwhile refugees fleeing Syria have told the Telegraph that regime militia are using rape and the threat of it to scare the opposition.
An activist calling himself Rami who has spent the past months helping families escape into neighbouring Jordan said: "There was a 17 year old boy. He was in a terrible condition. He would sit and cry and refused to eat or speak to anyone," said Rami. "Eventually with the help of a councillor he opened up. He had been arrested at a protest. When he was taken to a detention centre two officers had raped him".
"I know of many cases like him. They would throw raped male protesters back out on the streets as a warning to others," said Rami.
Rami is a wanted man by the regime. Months earlier he was forced to flee his home town of Dera'a leaving his wife 'Hadija' alone at home with their five children.
Late one night, ten 'shabiha' [government paramilitaries] broke into the bedroom where she and her daughters were asleep.
"They tore at my nightgown trying to strip me. I started screaming. My daughter was crying," said Hadija. "They were taking videos and photos on their phones".
The men only fled when neighbours who heard the commotion intervened.
A week later four of them returned. "I promised that my husband would hand himself him," said Hadija. "They said; 'Tell your husband that we have seen your breasts and we have stripped you. Next time we are going to rape you and we film it and air it everywhere'".
Terrified, she gathered her children and fled to stay with relatives on the outskirts of the city, never staying in one home for more than a few days.
"They [security forces] did the same with many others. It became known that the sister, wife, or daughter of anyone who was fighting might be raped, and many were," said Hadija. "Now those who are wanted take their wives and daughters with them."
The situation is worse in Baba Amr, the former rebel bastion that was crushed by regime forces, said refugees in Jordan.
"In Homs they treat the women as spoils of war," said Fathima, who fled from Baba Amr.
Fathima's husband had been leading a rebel unit in Baba Amr when the district fell and soldiers began conducting house-to-house raids. Hurriedly she hid her husband, children and thirteen year old brother in law in a secret cranny in their home before opening the door.
"One of the men wanted to see inside the pantry. Then he grabbed me hard by the hand and tried to drag me inside. I resisted, I was praying, "in God I put my faith" out loud. I freed my hand but he grabbed me by the waist. He tried to rip my clothes away," said Fathima.
"I didn't want to scream because I knew my husband would come and then they would kill him".
On this occasion Fathima said she was saved when another soldier who shouted at the men to leave the house. Others were not so lucky she said; "It is common in Homs. Relatives on my husband's side were found killed, among them Hameda, a 17-year-old girl, who had been raped".
Documenting cases of rape against women is extremely difficult in Syria's conservative society where a family's honour is tied to the virtue of its women. The mere suggestion of compromised chastity, no matter the circumstance, is a stain that can make the victim and her entire family outcasts.
Particularly in rural communities in Syria, the mere threat that women may be being raped is having terrible consequences.
"We know of cases where husbands have divorced their wives, casting them from their homes, just because they were taken to a detention centre and so might have been raped," said a Syria researcher for the global campaign group Avaaz.
"This is happening but it is not something people talk about. Women who were raped can no longer get married. Their life went like that," said Hadija snapping her fingers together.