The concerns have run the gamut from legitimate to outlandish, all generated by the lack of clarity offered by the team and Mauer. With that in mind, the star catcher met with reporters on Friday in hopes of alleviating some worries, dismissing some rumors and ensuring the fans that he will be ready to go next season.
"I'm healthy, I'm happy," Mauer said. "I can rule out crazy things I've heard like Lyme disease, Lou Gehrig's disease, rheumatoid arthritis, Lupus. I think we've heard it all. I don't have any of those things."
The rampant speculation swirled all season long, both inside and outside the Twins' clubhouse. Mauer played in only 82 games, missing most of the first two months of the season with a condition the team initially called "bilateral leg weakness." He also missed time because of a viral infection and an upper respiratory infection that turned into pneumonia and ended his season in mid-September.
Through it all, the 2009 AL MVP hit just .287 with three home runs and 30 RBIs in the first season of an eight-year, $184 million contract extension. As the losses piled up and the Twins sunk into the AL Central basement, Mauer took the brunt of the criticism for the first time in his career.
Mauer mentioned several times that there were some things he wished he would have done differently while last season was unfolding, most notably "the message to the fans and what really was going on. It was kind of a big mystery. I think I tried to correct that. It just didn't really work out."
Mauer said he is fully recovered from pneumonia and plans on being ready to go as soon as the Twins report to spring training in February.
It all started in spring training last year after Mauer had minor knee surgery in December. He hardly played in the exhibition season, electing to work out and save his legs for the rigors of catching in a 162-game season.
But he only played nine games in the opening month of the season before landing on the disabled list with the eyebrow-raising leg weakness diagnosis. He didn't return until the middle of June, then labored through another three months before going on the disabled list for good on Sept. 14 with the illness.
His once sterling image in his hometown was tarnished by the situation, with fans booing him on occasion and teammates wondering exactly what was wrong with the All-Star.
"We've had kind of a tough year collectively," Mauer said. "I think when that happens, you just try to right that ship. I don't think (my teammates) really knew what was going on. Maybe that was part of the frustration, too."
It was an entirely new experience for Mauer, who grew up in St. Paul and had been idolized by fans ever since he was a multi-sport prep star at Cretin-Derham Hall High School.
"I think what surprised me a lot was a couple things out there questioning my work ethic and that bugged me a little bit because I think guys who have been around know how hard I work and how much time I put in to what I do," Mauer said. "So that's one thing that frustrated me a little bit."
Mauer made several trips to the renowned Mayo Clinic in Rochester to get checked out, only increasing the concern among fans that something more serious was affecting him. But Mauer said he's been given a clean bill of health and he plans to be ready to go full throttle when spring training opens in February.
If he's learned one thing through the ordeal, it's that keeping the lines of communication open -- with the media, fans and his teammates -- is important to make sure nothing is misconstrued.
"I just feel that, and I've told people in the organization this, if I'm not out there playing, the fans should know why," Mauer said. "People are going to have their own opinions and you can't control that. As long as my family, my friends and the organization know what's going on, that's what's important to me."
Mauer said his knee and legs feel good and he is making some changes to his workout and eating habits this offseason to try and be better prepared for the season. He still sees himself as a full-time catcher and is determined to help make sure the 99-loss season last year was a one-time setback.
"The best barometer is the player himself," GM Terry Ryan said. "If he feels good, then I feel good.
"You can talk to all the medical people you want; talk about what he's had and what's he's gone through and experienced, but if you ask the player and he tells you that he feels good, that gives you a pretty good sense things are going right."