other, more centralized polities of the Early Modern Era, where rulers were able to use royal authority to advance the interests of their own state religion, in the Holy Roman Empire religion was tied to the interests of the various princes, some of whom advanced Protestantism and others who advanced Catholicism within their own domains. In addition, there were the Hapsburg Emperors themselves.

So far, this explanation has largely been focused on the role of religion, but politics should not be overlooked either. Political centralization and religious uniformity often went hand in hand. Using royal authority to support or impose a state religion simultaneously served to advance the power and authority of the crown itself. This was also the case with the Emperor Ferdinand II: by advancing Catholic interests, he was also advancing his own political interests over competing power structures.

Ferdinand II had only recently inherited the Bohemia before succeeding to the position of Emperor. In seeking to impose Catholic supremacy through the suppression of Bohemian Protestants, he instigated a political crisis, where Bohemian Protestants ultimately rose in rebellion against the Emperor, offering rulership of Bohemia to the Protestant Frederick. From here the conflict would escalate, sparking a war that would devastate much of Central Europe.

The Thirty Years War was an exceptionally bloody war that was ostensibly fought over religion; however politics was a more important factor.

There were growing political and religious tensions between the Protestant and Catholic princes of the Holy Roman Empire. In 1608, the Protestant Princes formed the Protestant Union; in response the Catholic Princes formed the Catholic League in 1609. Each side vowed that there would be no territorial gain by the other.

On May 23, 1618, a meeting was held in Prague between Protestant Officials and officials of the Holy Roman Emperor who were Catholic. The dispute became heated and the Protestant delegates ended up pushing the Catholics out a window where they fell seventy feet into a moat filled with latrine waste. This "defenestration of Prague" was the immediate cause of the declaration of war; but the causes were the ongoing religious and political rivalries in the Empire.  

The Thirty Years' War was unleashed in the Holy Roman Empire: a collection of disparate states, principalities, and even free cities, under the nominal leadership of the Holy Roman Emperor. As the previous Educator has already mentioned, with the Peace of Augsburg, the choice to remain Catholic or turn Protestant was left with each of the individual princes, and this meant, in practice, that religion in the Empire was a bit of a political mess.

Furthermore, it is important to be aware of the level of religious intensity unleashed by the Protestant Reformation in Europe. Keep in mind, we're looking at the era of the Wars of Religion and the Witch Craze, just to give a few examples: religion was a much more powerful force in people's lives than it is in modern secular society, and the presence of these religious divisions inspired a lot of sectarian violence. Such violence was even instigated by the State itself.

The Thirty Years' War stemmed out of the actions of the Catholic Emperor, Ferdinand II, who had just inherited the crown of Bohemia. Ferdinand sought to impose Catholicism on his subjects by suppressing the Protestant population in Bohemia. In response to this religious suppression, the Protestants of Bohemia revolted against the Emperor and made overtures to the Empire's most powerful Protestant prince, Frederick of the Palatinate, offering him the Bohemian crown if he would support them against the Emperor.

The Thirty Years War was a devastating religious war in Europe in the early seventeenth century. It was the bloodiest war in Europe until World War II, with as much as one third of the population killed and hideous atrocities.

The war was the result of increasing tensions in the Holy Roman Empire between Protestants and Catholics. Attempts had been made to negotiate settlements, but the Protestant side had only been represented by Lutherans. Calvinists did not consider themselves bound by the terms, and problems ensued. In 1608, a series of Protestant states (that is states within the HRE) formed the Protestant Union. The Catholic states returned the favor by forming the Catholic League in 1609. Each of the two groups was determined to stop the other from territorial gains.

The fuse that began the war was a strange situation known as the "Defenestration of Prague," when at a meeting to protest government action, several Protestant officials seized two Hapsburg (and therefore Catholic) officials and threw them out a window into the moat seventy feet below. They were only saved because the moat was also a latrine dump.

The war is typically divided into four phases: Bohemian, Danish, Swedish and French. The distinction is to complicated to explain here; but the links below can provide more detail. By the last (French) phase, the war was no longer over religion, but over territory. Throughout the war, there were numerous atrocities, such as the following description written by an eye witness:

T]he soldiers stretched out a hired man on the ground, stuck a wooden wedge in his mouth to keep it open, and emptied a milk pail full of stinking manure droppings down his throat—they called it a Swedish Cocktail. Then they used thumb-screw which they cleverly made out of pistols, to torture the peasants….They put one of the captured bumpkins in the bake oven and set fire in it…I cant say much about the captured wives, hired girls and daughters because the soldiers did not let me catch their doings. But I do remember hearing heir pitiful screams in various dark corners.

The war ended with the Peace of Westphalia which among other things, left France the strongest country in Europe. I urge you to read the links below for more information.

There were several conflicts that comprised the Thirty Years' War, and they had many different, specific causes. This answer will therefore only deal with the more general causes. The fundamental cause of these conflicts was unresolved tension between Catholics and Protestants in Europe, especially within the dozens of German principalities. The peace of Augsburg had sought to alleviate these tensions, but failed for a number of reasons, including the rise of Calvinism. The other general cause of the Thirty Years' War was, again very generally speaking, a series of dynastic and territorial struggles, again involving contested areas within Germany. These squabbles pulled in, at various points, the Spanish Habsburgs, Swedish, French, and Danish monarchs, and a number of lesser rulers. Their aims varied, and were usually related to advancing dynastic claims.

In the short-term, the consequences of the Thirty Years' War were utterly disastrous. This epic conflict wrought devastation on Europe, causing death and suffering on a massive scale. Somewhere in the region of 8 million people died—most of them through the ravages of famine and disease rather than injuries sustained on the battlefield. The whole nature of war had been changed, with civilian populations becoming embroiled in the thick of conflict in a way that was hitherto unprecedented. The Thirty Years' War wasn't simply fought on battlefields between professional soldiers; it spread out into towns, villages, and cities, causing enormous suffering among the civilian population.

In the long-term, the Thirty Years' War laid the groundwork for the formation of the modern nation-state. After the signing of the Peace of Westphalia, which formally ended the conflict, the precise boundaries of each territory became much clearer. The position of the nation-state was further strengthened by a corresponding diminution in the political power of the various Christian churches. Bitter religious differences had led to the outbreak of the Thirty Years' War, but from this point on, the religious policy of each European power would be firmly decided by the secular authorities. This ensured that religious differences would never again plunge Europe into such an appalling period of bloodshed and chaos.