All ten Super League teams and fifteen Challenge League clubs (FC Vaduz are from Liechtenstein and thus play in the 2009–10 Liechtenstein Cup) entered this year's competition, as well as thirteen teams from 1. Liga and 26 teams from lower leagues (their level within the Swiss league pyramid is given in parentheses below). Teams from 1. Liga and below had to qualify through separate qualifying rounds within their leagues.
Teams from Super League and Challenge League were seeded in this round. In a match, the home advantage was granted to the team from the lower league, if applicable.
The winners of Round 1 played in this round. Teams from Super League were seeded. In a match, the home advantage was granted to the team from the lower league, if applicable.