* Nuns appear at thanksgiving service in Damascus
* 15 women released from government detention
* Fate of more than 100 other political prisoners unclear
By Marwan Makdesi and Khaled Yacoub Oweis
DAMASCUS/AMMAN, March 10 (Reuters) - Thirteen Greek Orthodox nuns arrived in Damascus on Monday after al Qaeda fighters who held them for more than three months freed them in a deal providing for the release of women prisoners held by President Bashar al-Assad's government.
It was not clear how many women prisoners had been freed. Activists said at least 15 were released from Adra prison north of Damascus, just a fraction of the 153 which some officials had said would be included in the exchange.
The mostly elderly nuns and three other women from their convent seemed in good health as they sat in a room in Damascus with several other Christian clerics. Most of them were dressed in black habits and wore large crosses around their necks.
"All of Syria is happy today (for their return)," Bishop Luka al Khoury told Reuters. "These are women who do nothing but pray...They don't have weapons or bombs. On the contrary, they pray for people to be safe and secure."
Eleven of the nuns later attended a service of thanksgiving for their safe return at the Greek Orthodox Church of the Holy Cross in Damascus. Mother Superior Pelagia Sayyaf, one of the abducted nuns, held a candle and wept as she entered the church.
The Greek Orthodox Patriarchate welcomed the nuns' return and called for the release of all remaining prisoners in Syria's civil war, including two prominent Syrian bishops who were abducted in Aleppo province last April.
The nuns went missing in December after Islamist fighters took the ancient quarter of the Christian town of Maaloula north of Damascus. They were later moved from their monastery of Mar Thecla in Maaloula to the rebel-held town of Yabroud, about 20 km (13 miles) to the north, which is now the focus of a government military offensive.
Witnesses said the captives were released just over the border in Lebanon on Sunday before returning to Syria via another route under government control. (ID:nL6N0M60NP)
An online video showed the nuns being transported in 4x4 vehicles by masked gunmen waving the banner of the Nusra Front, al Qaeda's affiliate in Syria. In another video, one of the nuns said the rebels took care of them and did not subject them to any mistreatment.
Activists said Syrian government authorities released 15 women activists who had been held on terrorism charges at the sprawling Adra prison on the outskirts of Damascus.
Anwar al-Bunni, a prominent human rights lawyer in Damascus whose family was representing some of the women, said one of them had been serving a 20-year sentence.
Many had been sentenced under laws against terrorism enacted after the revolt against Assad erupted in March 2011, while others were being held without charge, he said.
"We are hearing that a swap is under way. We ascertained that 15 women have been released so far because they were held in a formal prison. It is unclear till now what happened to the rest," said Bunni.
Activists said more than 100 other women detained in secret police and intelligence compounds, including several imprisoned with their children, were still awaiting release.
Qatari Foreign Minister Khaled al-Attiyah, who said his country's mediation had secured the nuns' release, told state news agency QNA that the exchange deal included the release of 153 female Syrian prisoners from state prisons.
Syrian Information Minister Omran Zoabi told the state news agency SANA that 25 people "whose hands were not stained with the blood of the Syrian people" had been freed but had chosen to stay in Syria and rejoin their families.
He denied that there had been any direct or indirect contact between Syria and Qatar on the issue of the nuns' release, and said such talk was "an attempt to promote some ideas, poison the atmosphere and provoke public opinion".
The Syrian Observatory for Human Rights, an anti-Assad monitoring group, said witnesses at the border where the nuns were released had seen four buses carrying the women prisoners but it was unable to confirm their current whereabouts.
Reuters could not independently confirm these reports, and there was no comment from the Syrian authorities.
Opposition activists say they have gathered the names of 60,000 people who have been detained by security forces since the revolt, including 3,000 women and children. Most of the prisoners had protested peacefully, they said. Loyalists, including members of Assad's minority Alawite sect, have been also kidnapped, but authorities have not released any numbers.