"I can't really characterize it as pain versus discomfort versus typical soreness," Alderson said Tuesday afternoon. "Whatever it is, it's sufficient in nature that he wants to have it checked."
The Mets plan to remove Santana from his current Minor League rehab assignment, which began last Thursday with three scoreless innings for Class A St. Lucie. Though the results from Santana's scheduled Thursday examination will determine how soon -- if at all -- he can resume pitching in Minor League games, the Mets will prevent him from doing so at least until next Monday, in order to establish a new 30-day rehabilitation period.
"Right now, it's a matter of Johan proceeding at his own pace," Alderson said. "He's going to have to be sensitive to how his body responds to increased workload. I wouldn't say it's something that we expected to happen, but I think in the overall course of things, it's probably not something that should be unexpected."
Undergoing surgery last September to repair a torn anterior capsule in his left shoulder, Santana began throwing a baseball in February before first stepping onto a mound in June. Monday's rehab start marked the beginning of a sequence that put him on track to return to the Mets in late August; now, it is unlikely that he will be able to pitch in the big leagues before September at the earliest.
"I think he has less confidence than he might have had, so I think it's prudent to have him checked out," Alderson said. "It will either be reassuring or we'll step back and see where we are."
When healthy, Santana has given the Mets a strong return on their six-year, $137.5 million investment, producing a 40-25 record with a 2.85 ERA over his first three seasons in New York. But he has also displayed evidence of a deteriorating body; Santana underwent right knee surgery following the 2008 season and ended his '09 season with a left elbow scope.
He remains under contract for at least the next two seasons, with a $25 million team option for 2014.
Santana's teammates saw firsthand last weekend how difficult his most recent operation can be to overcome. One of the two most prominent pitchers to undergo the relatively rare procedure, Nationals right-hander Chien-Ming Wang gave up six runs to the Mets on Friday in his first big league start in more than two years. The game's other prominent test case, former Cubs All-Star Mark Prior, has not pitched since undergoing anterior capsule surgery in 2008.
Given those precedents, Alderson has been careful to classify Santana's rehab as nothing more than a step toward 2012. The Mets will not be overly concerned if Santana does not pitch this season, he said, because their sole goal is to have him healthy for next year.
"Nothing is worth it to the point that we're going to push him to do something he's not capable of doing," Alderson said. "I've already said that as far as 2011 is concerned, we're not looking for him to contribute to a pennant race. So we will look at September as part of his overall recovery from the surgery."