The fundamental cause was the internal decay of the empire from 1555, as evidenced by the weakness of the imperial power, by the gross lack of patriotism manifested by the estates of the empire, and by the paralysis of the imperial authority and its agencies among the Protestant estates of Southwestern Germany, which had been in a state of discontent since 1555. Consequently the whole of Germany was in a continual state of unrest. The decay of the empire encouraged the other nations of Western Europe to infringe upon its territory. Spain and the Netherlands made use of the period of the twelve-years truce to secure a footing in the neighbouring district of the Lower Rhine so as to increase their strategic base. For nearly a hundred years France had made treaties with many of the estates hostile to the emperor. Henry IV of France was murdered in 1610 at the very moment he was about to interfere in the war over the Jülich-Cleve succession. James I of England was the father-in-law of the head of the Protestant party of action in Germany, Elector Frederick V of the Palatinate, and was inclined to take part in a continental quarrel. Denmark sought obstinately to obtain the power of "administration" over the dioceses of Northern Germany that had become Protestant, and to get control of the mouth of the Elbe. Gustavus Adolphus (1611-32), of Sweden, also showed a strong desire to interfere in German affairs. At the outbreak of the Thirty Years War all these countries, it is true, were prevented from taking part in it by internal difficulties or by wars in other directions. Still the disposition to do so existed everywhere.

Another cause of the war was that the countries forming the Austrian provinces belonged to the empire. For, in the first place, the empire, owing to the geographical position of these countries, became involved in the contemporary affairs in Eastern Europe. The general aristocratic reaction that appeared throughout Europe at the end of the fifteenth and in the sixteenth centuries gradually became so powerful in the eastern and northern countries that a life-and-death struggle between its representatives and the sovereign power broke out at the beginning of the seventeenth century in the more active districts of these sections. These causes gave the first impulse to the Thirty Years War (see section II below). In addition the dynasty ruling the countries forming Austria was a branch of the Habsburg family, whose most distinguished line at that era ruled Spain. From the reign of Philip II (1556-98) the Spanish Habsburgs were the champions of Catholicism in Western Europe and the chief rivals of France in the struggle for supremacy in Europe. From about 1612, especially during the administration of Philip IV (1621-65) and his distinguished minister Olivarez, they displayed increased energy and tried to induce the German Habsburgs to support their plans. The empire was all the more affected by this Spanish policy as the head of the German Habsburgs was Emperor of Germany.

A further important cause was the religious sectarianism which, after diminishing for a short time, grew more intense early in the seventeenth century. In the Catholic movement (about 1592) which followed the Council of Trent only Catholic theologians and a few princes had taken part; the second movement, on the contrary, carried with it the masses of the clergy and laity, and was marked by an ardent spirit of faith and a passionate demand for the spread of Catholicism. If among Protestants the idealistic enthusiasm was perhaps not so great, still their partisan feeling was equally violent and their combativeness no less ardent. After the war began it soon became manifest that social and economic reasons made Germany a favourable soil for its growth. Economic life, which for a long time had flourished greatly, from the second half of the sixteenth century had grown stagnant. Consequently there existed a large number who were glad to have the opportunity of supporting themselves as paid soldiers and of enriching themselves by plunder. The nobles, also, who were numerous in proportion to the rest of the population, took advantage of the opportunity to indulge their private feuds and robberies. As only a small number of them were attracted by foreign wars, they were ready therefore for internal disorders. Soon there appeared leaders of ability who gathered both nobles and burghers under their banners and retained them in their service by indulging their evil instincts. On the other hand, the people of Germany, who had been long unaccustomed to war and were not trained to bear public burdens, chafed under the hardships now imposed upon them. This discontent, combined with the ease with which troops were equipped, aided in prolonging the war.