Practised by about an equal number of people, the two main religions in Bosnia and Herzegovina are Islam and Christianity, both of which have a long history in the Balkan region. Over the centuries, Christians and Muslims have intermarried freely in Bosnia and Herzegovina.

People in the region converted to Christianity around the 9th century. Today, the most important churches are the Eastern Orthodox and Catholic. Eastern Orthodoxy arose from the Great Schism of 1054, when church authorities in Rome and Constantinople disagreed and the two churches of Roman Catholicism and Eastern Orthodoxy were created. Although the churches share many similarities, the Orthodox Church argues that it practices the original Christian faith; priests are allowed to marry, and the Virgin Mary is not revered as an icon, as she is in Catholicism.

Because the Balkan region was the fault line between the western and eastern Roman Empires, some Slavs received Eastern Orthodoxy from the Eastern Roman Empire (Byzantium), while others joined the Roman Catholic Church. Today, Catholicism is the faith of most Croats, while Serbs practise Eastern Orthodoxy. During Turkish rule, both churches were important protectors and preservers of Slavic language and culture.

Islam arrived in the Balkans in the 14th century with the invading Turkish Ottoman Empire, and many Bosnian Christians converted to Islam during the centuries of Turkish rule. Islam is based on the Koran, the teachings of Mohammed, a 6th century prophet who claimed to be the last in a line of prophets that include Jesus, Abraham and Moses. Muslims follow the five pillars of Islam: profession of the faith, which says that Allah is the one God and Mohammed his prophet; daily prayer; taxes for the upkeep of the poor and religious scholars; fasting during the month of Ramadan; and, if possible, the hajj (pilgrimage) to the Holy City of Mecca, Saudi Arabia, once in a lifetime. Muslims also kneel so that they are facing the direction of Mecca whenever they pray.

The first traces of the Jewish community existence in Bosnia and Herzegovina originate from the mid-16th century. Probably there were Jews in the country earlier. Jewish communities thrived in the country until the Second World War.

Bosniaks, the ethnic name for Muslim Slavs, practise a somewhat different form of Islam than is found elsewhere. For example, women wear Western-style clothing, though some cover their heads with scarves, especially on religious occasions. Some Bosniaks also drink alcohol, which is officially forbidden to Muslims.

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Bosnia and Herzegovina formerly had a thriving Jewish community. The illustrated Sarajevo Haggadah (Passover Book) is housed in the National Museum.

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Sarajevo used to be considered the seat of Islam in the west. The city has 73 mosques by the Miljacka River, although some of these were destroyed during the war.