The rights group said on Wednesday that the militants have attacked religious sites in the provinces of Latakia and Idlib.
A Shia place of worship was destroyed by the militants in Idlib, while two Christian churches were looted in Latakia, HRW said.
Human Rights Watch further stated that Syria’s opposition has failed to control the armed militants who are engaged in “looting and other criminal activities, like kidnappings.”
“Syria will lose its rich cultural and religious diversity if armed groups do not respect places of worship,” said Sarah Leah Whitson, the Middle East director at HRW.
“Human Rights Watch researchers observed what appeared to be deliberate damage to the local Husseiniya, a Shia place of worship,” caused by the militants after they entered the village of Zarzour in December.
Syria has been experiencing unrest since mid-March 2011. Many people, including large numbers of security personnel, have been killed in the violence.
According to a UN report, extremist militants from nearly 30 countries have been filtered into Syria to fight against the government.