There have been many religious wars through out history but upon analysis seldom were the wars based solely upon religious issues.
One example was the Thirty Year's War, which took place from 1618-1648 and involved most of the major European powers of the time. It has been considered a religious war because the increase in religious intolerance and religious rivalries was the main cause of the war but as the war progressed it became less about religion and more about territory and dynastic issues. The war can be broken down into four distinct periods ( Bohemian, Danish, Swedish, and Swedish-French)and the relative importance of the religious rivalries and dynastic ambitions were different for each period. Religion was the primary cause of the war during the Bohemian period (1618-1625). This is not to say that some dynastic ambitions were absent. It started when King Ferdinand a catholic was crowned king of Bohemia.
Most Bohemians were Protestant and were upset with King Ferdinand's intolerance with there religious beliefs. King Ferdinand was a —— catholic who wanted to restore Catholicism throughout the empire. Two years later he became Emperor of the Holy Roman Empire which alarmed protestants who thought they would lose there religious rights. Because of this Bohemians rebelled and deposed Ferdinand and named Frederick V as king.
Ferdinand financial help from the Pope, Spanish troops and troops from Catholic Bovaria defeated Fredrick the fifth at White Mountain. Emperor Ferdinand regained the Bohemian Throne and re-catholicization of Bohemia began. During the Danish period (1625-1629) Religion was a factor in the war however the Dynastic ambitions of Ferdinand and of the king of Denmark was the primary factor. The King of Denmark at the time was fearful that the power of the Habsburgs where getting to strong. The King also wanted to expand his territory and gain control over the Elbe River. The king of Denmark .