The explosions killed 47 pilgrims, majority Iraqi Shiites, and 12 Syrian pro-government fighters, Observatory chief Rami Abdel Rahman said.
Syrian state television said 40 people were killed and 120 wounded by "two bombs detonated by terrorists", while Iraq's foreign ministry said 40 of its nationals had died. The cemetery is one of Syria's most ancient and is where many prominent religious figured were buried.
There are 11 Shiite shrines in Bab al-Saghir cemetery, usually a visiting spot for Shiite visitors.
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Shoes, glasses and wheelchairs lay scattered on ground covered in blood.
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A number of the pilgrims had been brought by bus to visit the Bab al-Saghir cemetery and a shrine nearby when a bomb went off at the bus station. The then-named Jabhat Fateh al-Sham said it was behind that attack. Arab TV Al-Mayadeen also reported at least 40 were killed while the area was under tight security.
Last year, ISIS claimed responsibility for deadly attacks near the revered "Lady Zeynab" Shiite Muslim shrine on the southern outskirts of Damascus.
Earlier in January 2017, twin suicide bombings in the high-security Kafr Sousa district of the capital, killed 10 people, eight of them soldiers.
The ministry also calls on the worldwide community to denounce the terrorist crime that targeted Iraqi civilians visiting the holy shrines, it added. Iranians and other Shiites from Asia are often also among the pilgrims to the area. The Assad government views all armed opposition as terrorist groups.