The main cause was dissolution of the Yugoslavia which happened in 1990/1. Yugoslavia at the time was heavily influenced by Serbian politicians and also faced heavy economic downfall, so it doesn't surprise that it broke apart. Let me explain:

Dissolution brought a rise of nationalist politics on all sides and it first exploded with Homeland War of Croatia versus Yugoslavia where Massacres of Škabrnja and Vukovar happened on 18.11.1991.

Secondary cause Those were result of revival of Chetnik movement in Serbia that wanted to create Greater Serbia. Idea of Greater Serbia was born with Načertanije (or Script), a programme that written by Ilija Garašanin in 1844. Garašanin claimd that "A plan must be constructed which does not limit Serbia to her present borders, but endeavors to absorb all the Serbian people around her." The plan was kept secret until 1967. Further development was made by Vuk Karađžić, creator of modern Serbian language. He claimed, in his book Serbs All and Everywhere, that "There are at least 5 million people who speak the same language, but by religion they can be split into three groups ... Only the first 3 million call themselves Serbs, but the rest will not accept the name." Those ideas were main creator of Serbian politics in the '90s. With Orthodox faith as a driving force for a way to gain more territory under impression that all Orthodox Christians are Serbs.

Cause in Bosnia After Croatia, Slovenia and Macedonia seceded Bosnia was next, but in Bosnia large portion of country seceded from Bosnia and called themselves Republika Srpska (Serbian Republic/ Do not confuse it with republic of Serbia or more commonly known Serbia). That move had large negative reaction with Bosniaks (Muslims) and Croats (Catholics) that for a brief period joined forces to fight Serbs. Later there would be Free For All type of war, until Bosniaks and Croats don't join forces again.

Cause in Kosovo Kosovo population is split between Serbs and Kosovars or Albanians. With other Federal republics seceding from Yugoslavia Kosovars wanted to do the same which Serbs did not take lightly so they decided to go in and attack Kosovo.

TL;DR : Nationalistic policies and religion made clusterfuck.