Joe Mauer's controversial, injury-and-illness-filled season is likely over with less than two weeks left on the schedule.

The Twins catcher has been diagnosed with mild pneumonia, the latest in a string of health issues that has hindered the former American League MVP and batting champion -- and the club. He has been told by doctors that he needs two weeks of rest. The Twins have 14 games to play over the next 13 days, not enough time for him to recover and see any action before the season ends.

Mauer's goal was to play as much as possible over the final two weeks of the season and then head into the offseason determined to change his conditioning program and return for 2012 in excellent shape. Instead, he exits in September the same way he began the season in April -- laid out by illness.

"He's pretty upset,'' Twins manager Ron Gardenhire said. "He's sick right now, but in talking with him today, he's not very happy. He's pretty upset. He's going to have to do what the doctors say. we all know those things, and take care of himself physically.

Barring an unforeseen speedy recovery. Mauer will end the season with a .287 batting average, three homers and 30 RBI in 82 games. It will be the fewest games he has played in a season since 2004, when knee surgery limited him to 35 games. He missed 58 games during the season because of leg weakness.

Mauer was not at the ballpark Friday, and it is unknown when he will return as he attempts to recover.

The latest episode in Mauer's season of woe began Sept. 2, when he got sick during a series against the Angels in Anaheim, Calif. He was diagnosed with an upper respiratory infection. He added that he had fluid in one of his ears and was having "episodes of vertigo.''

"Despite medication, his symptoms have not resolved,'' Twins trainer Rick McWane said. "In Kansas City [this week], he started to complain of a persistent cough.''

When the Twins returned from their 0-5 road trip, Mauer headed to the Mayo Clinic in Rochester for more tests. That was when he was diagnosed with mild pneumonia, also referred to as walking pneumonia. The website WebMD describes it as the least scary kind of pneumonia, "because it's a mild pneumonia and does not generally require hospitalization.''

But it's enough to likely end Mauer's season.

"The recommendation is medications and rest for two weeks,'' McWane said.

Mauer has had to answer many questions about his health this season. A viral infection in April forced him to lose 15-20 pounds. He also was shut down because of leg weakness at about the same time, missing 58 games from mid-April through June. In late April, he underwent a battery of tests that ruled out any serious illnesses.

Still, the questions about his health, work habits and perceptions that he is soft continued. In addition to changing his offseason workout program, he also agreed to be more available to discuss his issues.

But right now he can't implement any of those new policies as he recovers from his latest illness.

His season will be defined by his inability to stay in the lineup, multiple trips to the Mayo Clinic and failure to find the swing that got him three batting titles.

"He really, really is not happy about this situation,'' Gardenhire said. "He wants to be out there. He wants to be there with the guys. He's pretty upset about it, to tell you the truth.''