Doctors told Mauer he needs to rest for two weeks, which would mean he will miss the remainder of the season.
Mauer, the American League's MVP two years ago, signed an eight-year, $184 million contract prior to the 2011 season. After off-season knee surgery, he dealt with an assortment of illnesses and injuries, and played just 82 games this year. His .287 batting average and three home runs were career lows.
The diagnosis came from the Mayo Clinic after Mauer was slow to recover from an upper respiratory infection. He last played on Sept. 14.
During his MVP season, which came in his fifth year with the Twins, Mauer batted .365 with 28 home runs and 96 RBI.