The winner of 17 Grand Slam titles was not in the Swiss line-up announced on Monday for the first-round World Group match in Geneva on February 1-3.
The team consists of veteran Stanislas Wawrinka and little-known Marco Chiudinelli, Henri Laaksonen, Michael Lammer and Sandro Ehrat.
The Czechs are expected to be led by Tomas Berdych and Radek Stepanek, who helped beat Spain in the Davis Cup final in November.
Federer does not always play in the early rounds of the Davis Cup. The first round comes the week after the end of the Australian Open.
Berdych beat Federer in the quarter-finals of the US Open in September and the Wimbledon quarter-finals in 2010.