When the great thinkers of the Enlightenment, as well as their predecessors in Ancient Rome and Greece, and later modern thinkers and agnostics came up with the idea of secularism, they were motivated by the strong conviction that religion impedes human progress, being focused on dogma and superstitions, instead of reason and scientific method. Combined with John Locke’s writings on social contract and his argument that government had no authority over individual conscience, it resulted in the principle of division of church and state which would be independent from each other, first mentioned by Thomas Jefferson in his letter to the Danbury Baptists.

Those ideas brought about the concept of religious tolerance, freedom from religious rule and teachings and freedom from government imposition of religious beliefs in a state that is neutral on matters of belief and gives no privileges and subsidies to religions.

Religion being such an important aspect of human society and existence in general and being based on sets of narratives, symbols and practices, almost by default reserved great influence over the people for those who had the monopoly on interpretation of the will of deities and mediation of contacts of common people and laypersons with the usually unfathomable and unseen God (or gods and other deities). That influence naturally translated into great and very real political power, providing a tool for religious leaders to interfere in political affairs.

The secularism mentioned above is primarily European invention and the thinkers that developed the concept were influenced by the long history of religious warfare that ravaged Europe for centuries. Islam, on the other hand, was from the very beginning based on the principle of inseparability of religion and stage. All great Islamic states throughout history were theocracies. However, Islamic teachings and practice on treatment of followers of other religions (notably those mentioned in the Book – Judaism and Christianity) resulted in the Ottoman Millet system of separate courts pertaining to personal law allowing religious minorities to rule themselves, with Islam reigning supreme. The Millet system, many historians claim, meant that 16th Century Ottoman Turkey was far more tolerant, in terms of religious diversity than, for example, 16th Century France.

Matters of religious tolerance have always been important in the Balkans, a region where most of the great religions have come head-to-head at one point of time. The line dividing Western and Eastern Christianity passes straight to it, with Islam arriving later to the mix. In the lands under the Ottoman Empire, the Millet system meant that religious institutions were holders or real political power, effectively ruling legal matters of their constituencies. Later, during the struggle for national liberation, religious affiliation of the local population to one or the other Orthodox churches drew the lines of the newly emerging states as it was seen an integral part of the national identity of the various peoples.

Fast forward to the end of the 20th Century... The collapse of Communism coincided, it could be argued, with the rise of new religious fervour all over the world. The takeover of power of the Shiite Islamic theocracy in Iran, the issue of Islamic immigration in Europe and the rise of Christian Right in the U.S. and Islamic fundamentalism somewhat turned the tide at the expense of secularism. Samuel P. Huntington argued, in his Clash of Civilisations that cultural and religious identities will replace ideology of the Cold War as the main source of future conflict.

In the Balkans, too, religious revival was imminent. The numbers of people that declared themselves as, at least nominally belonging to one or the other confession grew, in spite of the fact that it wasn’t followed by a parallel rise in church attendance, and percentage of population that are regular churchgoers remains in the single digits. The wars of the Yugoslav succession were, in many aspects, religious in nature, with Catholics, Orthodox Christians and, Muslims identities often crucial to the conflict. Houses of prayer, primarily mosques, but also churches, were destroyed and big concrete crosses pepper the hills in BiH and Macedonia, as if to declare to the world that that was Christian land.

Religions, citing many trespasses against them by the former Communist regime, adopted a much more muscular stance in the fight for social and political influence, fiercely defending their turfs against attempts by other confessions, especially proselytizing protestant sects. Strong demands for restitution of property and introduction of state-sponsored religious education in public schools, open opposition to efforts to improve women and LGBT rights, have been seen in all of the countries in the region.

For overviews of the situation by individual countries, read the country reports: Albania, Bosnia and Herzegovina, Croatia, Macedonia, Serbia.