As hundreds emerged from a prison near Damascus dubbed the “human slaughterhouse,” Rim Turkmani waited anxiously, hoping her cousin detained eight years ago would be among the prisoners who emerged haggard but joyful.

“We’ve heard nothing about him since, except that he is held at Saydnaya prison,” she said of her cousin, Abdullah, who was just 18 when he was imprisoned for participating in the uprising against former President Bashar al-Assad.

Assad’s downfall has provided hope for the families of tens of thousands of Syrians who disappeared into the labyrinth of the country’s feared security apparatus in recent decades. Hundreds of men were freed from the notorious Saydnaya prison, about 20 miles north of the capital, after Syrians stormed the prison hours before Assad fled the country early Sunday.

Footage from inside the prison showed armed men shooting through locks and gaunt detainees emerging hollow-eyed and limping. “Ten years in prison!” cried one man in a video provided by the Association of Detainees and Missing in Saydnaya Prison. Another video showed a wall of screens that enabled guards to watch over the prisoners in their cells.

Prison

Wadha Ali Mohammed, mother of Joan Marwan Mahmoud, looks at a photo of her son who was imprisoned in Syria for 13 years and who was still alive when rebels opened the prison gates after entering Damascus, in Duhok, Iraq, December 9, 2024. REUTERS/Ari Jalal

Some relatives were convinced that more prisoners remained trapped in hidden subterranean cells. The Syrian Civil Defense, an independent rescue organization also known as the White Helmets, deployed wall-breaching specialists, iron door-opening crews and trained dog units to search for any secret chambers. The group also enlisted the help of guides familiar with the layout of the prison, while the rebel military command called on soldiers who worked at the prison to come forward with passcodes to unlock the doors of underground cells.

“We opened several areas inside the prison including the kitchen and the bakery, but we haven’t found anything yet,” said Raed al-Saleh, head of the White Helmets. “Until now, there is no evidence to confirm the presence of any prisoners other than those who came out yesterday.”

The desperate hunt for clues about missing relatives also risks damaging evidence of the regime’s crimes and undermining the quest for justice. As many as 13,000 people were executed in Saydnaya prison during the first six years of the uprising against Assad, which broke out in 2011, according to a report by Amnesty International. Many others were killed there after being repeatedly tortured and systematically deprived of food, water and medicine.

Intsar al-Jaber, speaks with Reuters TV as she awaits news to her 45-year-old brother and cousin who were imprisoned at Sednaya prison takes place, after rebels seized the capital and announced that they have ousted Syria’s Bashar al-Assad, in Sednaya, Syria, December 9, 2024. REUTERS/Amr Abdallah Dalsh

A report by the Syrian Network for Human Rights published earlier this year found that more than 96,000 people remained forcibly disappeared by the regime since 2011. Other parties to the conflict have also forcibly disappeared opponents, though the numbers are small in comparison. Islamic State forcibly disappeared nearly 9,000 individuals. Nearly 3,000 people have been forcibly disappeared by the U.S.-backed Syrian Democratic Forces, which control the northeast of the country. And Hayat Tahrir al-Sham, the U.S. designated terrorist group that spearheaded the rebel offensive and is poised to wield significant power in the new Syria, has forcibly disappeared more than 2,000 people.

Enforced disappearances peaked in 2012 as Assad sought to crush the revolt, which erupted after teenagers who had scrawled antiregime slogans on a wall emerged from prison with signs of torture.

While the volume of arrests decreased over time, a United Nations report found that mistreatment continued, with detainees electrocuted, beaten with pipes and subjected to sexual violence. Prisoners had their feet whipped and their teeth and nails pulled out. Some had their spine stretched while chained to the so-called German chair.

Rights watchdogs say torture is widespread throughout the Syrian detention system. Rebel forces broke open other prisons as they marched on Damascus, including in Aleppo and Hama.

“My father dared to demand freedom for Syria and has been detained for 12 years with no word about his fate,” said Syrian activist Wafa al-Ali after rebels seized the city of Hama last week. “Seeing detainees released from Hama prison breaks my heart and sparks dangerous hope.”

Among those released was a man who said in a video that he and more than 50 others were due to have been executed hours after rebels captured the prison where they were being held. Another had been detained 43 years ago when Assad’s father, Hafez al-Assad, was still in power.

Fatin Ramadan received a death certificate for her father several years after he was detained by Syrian security agencies along with her brother in 2012. But when she saw images of detainees who had emerged from the Hama central prison last week on social media, she thought she recognized her father.

People walk as the search for prisoners at Sednaya prison takes place, after rebels seized the capital and announced that they have ousted President Bashar al-Assad in Sednaya, Syria, December 9, 2024. REUTERS/Amr Abdallah Dalsh

“I thought he had come back from the dead and that the news of his death was false,” said Ramadan, whose father was imprisoned in connection with her own work treating people wounded in antigovernment protests. An artificial intelligence tool confirmed the man was her father, and she rushed to track him down—only to discover it was someone else.

As opposition forces advanced, Omar al-Shogre feared the guards would kill the detainees before surrendering Saydnaya. He was detained there himself after taking part in antigovernment protests and escaped in 2015 after his mother paid a bribe.

When Shogre was released, he had to sneak out of the country with no hope of returning as long as Assad remained in power. “Now, when a Syrian is freed he’s freed back to his country; he doesn’t need to flee anywhere,” he said.

In Saydnaya, frantic relatives went from cell to cell, checking graffiti on the walls for traces of their missing relatives, according to Diab Serriya, a founding member of the Association of Detainees and Missing in Saydnaya Prison, who was imprisoned there himself.

Some relatives broke into the prison administration and ransacked files seeking clues about the fate of the missing. Files were burned and rumors spread that loyalists might be trying to destroy evidence of the regime’s crimes, he said, urging rebel groups to impose order on the prison. He confirmed on Monday there were no more detainees left to be found there.

The White Helmets, who are conducting the search operation at Saydnaya, offered a reward of $3,000 to anyone who provides concrete information about the locations of secret prisons, promising confidentiality to members of regime security agencies. The group also urged desperate relatives to refrain from tampering with the prisons, warning they could destroy evidence needed to uncover the truth and support justice and accountability efforts.

“The fight in terms of bringing Assad down is over, but it’s not over when it comes to justice,” Shogre said. “We need to use the evidence we collected for 14 years to prosecute the criminals, because they cannot be among us in a free and democratic Syria.”

By late Monday, the chances that Turkmani’s cousin would emerge from Saydnaya appeared slim. Turkmani said he had initially been detained with his mother, who was tortured to pressure him into confessing to belonging to the armed opposition. After she was released, she refused to leave Homs with the rest of her family, so she would be there to open the door when Abdullah came home.

Write to Isabel Coles at isabel.coles@wsj.com