During the period from 1798 to 1815, the shape of Switzerland changed several times, sometimes as an act of policy, and sometimes according to the fortunes of war.

In 1798 the allied towns of Geneva and Mulhouse were incorporated into France. In 1802 Valais was detached from the Helvetic Republic. For a few years it was independent, but in 1810 Napoleon incorporated it into France as the Simplon Department. With Valais separated from Switzerland, the French had two important passes in their hands - the Simplon and the Grand St Bernard - and no longer needed the right to march through Swiss territory.

Switzerland also gained some territory: the former Austrian possession of the Fricktal on the Rhine just east of Basel. It was invaded by the French in 1799, but made part of the Helvetic Republic in 1802 as a separate canton. This arrangement was short lived, however: after the Act of Mediation it became part of the new canton of Aargau, and has remained so ever since.

Graubünden changed hands several times between the French and the Austrians in 1799-1800, but the French were eventually victorious and in 1801 Napoleon decreed that it should be Switzerland's 16th canton. Nevertheless, it did not get back its subject territories which Napoleon had incorporated into the Cisalpine Republic in 1797. These are still part of modern-day Italy.