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The release of the captured rebels took place in several cities throughout Syria.
The deal brokered by Doha and Qatar governments was criticized as severely disproportionate.
The Humanitarian Relief Foundation, a Turkish humanitarian aid group, is facilitating the exchange.
Reactions to the prisoner swap were largely positive. Iranian media hailed the process, with Tehran broadcasting images of the Iranians arriving at a hotel in Damascus where they were greeted by officials and relatives.
The Iranian government says the prisoners, abducted in August 2012, were pilgrims traveling to shrines revered by the Shia community in Damascus.
The Syrian opposition said they were members of Iran’s Revolutionary Guards aiding Syrian government forces.
Turkey’s Hurriyet Daily News reported that there were at least four Turkish citizens among the released rebel prisoners.
The New York Times quoted Turkish Prime Minister Recep Tayyip Erdogan as saying that he wished “many other innocent people, and people in need, to be released from Syrian jails without delay”.
Erdogan made his comments on the sidelines of an official visit to Nigeria.
The prisoner exchange comes three days after Syrian President Bashar al-Assad laid out a peace plan that included a national reconciliation conference, elections and a new constitution for his war-torn country.
During his speech, Assad but said he would not deal with “terrorists”.
Assad also thanked Iran for its support of his embattled government.
Details of the rebel fighters and where they are from were not released.