13 nuns and 3 maids held by Muslim rebels in Syria for more than three months have been released in a prisoner exchange between the warring factions. 

The nuns had been taken to the Lebanese town of Arsal earlier in the week and headed to Syria on Sunday accompanied by the head of a Lebanese security agency and a Qatari intelligence official.

They went missing late last year after Islamist fighters took the ancient Christian town of Maaloula north of Damascus.

Soon after the nuns disappeared from their Church in December, Islamist rebels said they had taken them as their "guests" and that they would release them soon.

After being held in the Greek Orthodox monastery of Mar Thecla in Maaloula, where the dialect of Aramaic that Jesus spoke is still used, they were sent to the rebel stronghold of Yabroud, about 20km to the north.  Yabroud, near the border of Lebanon, has been the focal point of intense fighting the last few days as the government tries to stomp out the opposition there. 

"We want to thank God, who made it possible for us to be here now," one of the Greek Orthodox nuns told reporters as she arrived in Syrian government-controlled territory.

She thanked Syrian President Bashar al-Assad and Qatari Emir Tamim Bin Hamad Al-Thani, a leading supporter of the opposition.  She also thanked Lebanon's General Security agency director Abbas Ibrahim, who negotiated the exchange.

Rebels affiliated with the Al-Qaeda Al-Nusra Front are thought to be responsible for the abduction.  The nuns report that they had been treated well despite earlier reports that said they were forced to remove their crosses. 

The nuns were exchanged for about 150 female detainees who were being held in Syrian government prisons. 

In Damascus, throngs of people came to the historic Church of the Cross on Monday to watch the nuns walk down the aisle holding candles, in a joyous homecoming.

Several of the churchgoers called the nuns' safe release and passage home a rare bright spot in the fog of war that has blanketed the region.

Syria's Christians make up around 10 percent of the country's population and they have tried to keep out of the three-year-old conflict. Fear of the Sunni Muslim-dominated rebels is widespread among most Christians in Syria, as the group has been targeted for its suspected sympathies with the secular government of President Assad.

Experts believe that nearly 150,000 people have been killed since the uprising against Assad's regime erupted in March 2011.

Another 2.5 million people have fled the country because of the fighting, and another 6.5 million have been displaced within Syria.