The 30 Years War was both a religious and a territorial conflict. Alliances shifted, but in its broad outline, it pitched the Holy Roman Empire and its Catholic allies against the other European powers. By the 17th century, the Empire was firmly in the hands of the Habsburgs, who also ruled Spain. France (though a Catholic country) was eager to break the power of the Empire and therefore gave its support to the Protestants.

The Confederation was able to keep out of the war largely because of the complex set of alliances the various member cantons had established in the second half of the 16th century. These alliances fell largely along confessional lines. Both sides realised that backing their co-religionists in the war according to their alliances would pull the Confederation apart.

However, on several occasions foreign Protestant forces violated Swiss neutrality by bringing their troops into its territory. The Confederation Diet eventually reacted by setting up a joint military council, with both Catholic and Protestant members, able if necessary to put up to 36,000 armed men on the border to prevent incursions by foreign troops. This arrangement, drawn up in 1647, was known as the "Defensionale of Wil".