Progressives and conservatives grew further apart during the 1840s. Their differences came to focus on the role and power of the Catholic church, and in particular of the Jesuits.

In 1844 Lucerne aroused consternation among progressives in many parts of the country by inviting the Jesuits to take over the administration of secondary education. Although the move was constitutionally perfectly legal, Radicals saw in it the long arm of the Pope, and some even tried unsuccessfully to overthrow the Lucerne government by force.

In response, seven conservative cantons - Schwyz, Uri, Unterwalden, Lucerne, Zug, Fribourg, Valais - secretly formed the so-called Sonderbund (= "separate league"), to protect their rights. However, they also turned to foreign powers to support them. When this became known in 1845, the liberals demanded its dissolution. But it was only in 1847 that there were enough cantons with liberal governments to tip the voting in the Diet. The Diet then declared the Sonderbund to be a violation of the Federal Pact.