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The extra work may have caught up with the affable infielder, who has played every position in the Majors except for center field and catcher.
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The 30-year-old Flaherty said he first noticed soreness last week.
"It's been sore for about five or six days," Flaherty said. "I was going to the training room, and they said, 'Take a couple of days and let it die down.' It feels fine. If I had to play, I'd play."
Flaherty said the shoulder doesn't bother him when he's hitting or fielding.
"Just throwing," he said. "I think making a lot of throws. It's nothing serious."
Without Flaherty, the Orioles still have options at third for now. Chris Johnson, who got the start Tuesday, has been a Major League third baseman for eight seasons. Paul Janish and Robert Andino have also played there in the big leagues.
Flaherty, who doesn't like to ask for a day off, admits that throwing from third base could be a reason why the shoulder is sore.
"It could be," Flaherty said. "One of the challenges of being a utility player, moving around, you're throwing from a lot of different angles. Kind of getting used to it every week, and just try to get ahead of it."
Flaherty expects to play Wednesday, when the Orioles host the Red Sox.
Rich Dubroff is a contributor to MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.