Crain was examined by team doctors Thursday, one day after he allowed six unearned runs in a 15-7 loss in Cleveland. A follow-up exam by a specialist in New York on Friday confirmed that Crain has a torn labrum and rotator cuff, leaving him unavailable for at least eight months.
New York Mets team orthopedist Dr. David Altcheck recommended that the 25-year-old Crain undergo surgery.
Twins manager Ron Gardenhire said the exam confirmed the team's diagnosis.
Crain was 1-2 with a 5.51 ERA in 18 appearances this season. In 2006, he went 4-5 with a 3.25 ERA in 68 outings.
A team spokesman said Crain will take a couple days to consider his options before making a decision about surgery.