Generally speaking, in most of the following cases, religion is both the stated cause of the killing and the only substantive difference between the two opposing groups. Obviously, there would be many additional conflicts where religion is just one of several divisions.
Albigensian Crusade, 1208-49
Algeria, 1992-
Al Qaeda, 1993-
Arab-Israeli Wars, 1948-
Arab Outbreak, 7th Century CE
Aztecs
Baha'is, 1848-54
Bosnia, 1992-95
Boxer Rebellion, 1899-1901
Christian Romans, 30-313 CE
Croatia, 1991-92
Crusades, 1095-1291
Dutch Revolt, 1566-1609
English Civil War, 1642-46
Holocaust, 1938-45
Huguenot Wars, 1562-1598
India, 1992-2002
Indo-Pakistani Partition, 1947
Iran, Islamic Republic, 1979-
Iraq, Shiites, 1991-92
Jews, 1348
Jonestown, 1978
Korea, 1700s
Lebanon, 1860, 1975-92
Martyrs, generally
Molucca Is., 1999-
Mongolia, 1937-39
Muslim conquest of India, 11th-17th C
Nigeria, 1990s, 2000s
Northern Ireland, 1974-98
Russian pogroms, 1905-06, 1917-22
St. Bartholemew Massacre, 1572
Shang China, ca. 1300-1050 BCE
Shimabara Revolt, Japan 1637-38
Sikh uprising, India, 1984-91
Spanish Inquisition, 1478-1834
Taiping Rebellion, 1850-64
Thirty Years War, 1618-48
Vietnam, 1800s
Witch Hunts, 1400-1800
Xhosa, 1857
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