| Andy Pettitte | P | 5/17/2013 | on 15-day DL | Strained left trapezius muscle |
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| Chris Stewart | C | 5/16/2013 | day-to-day | left groin injury |
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| Eduardo Nunez | SS | 5/6/2013 | on 15-day DL | Left ribcage strain |
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| Kevin Youkilis | 3B | 4/28/2013 | on 15-day DL | Lumbar spine strain |
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| Joba Chamberlain | P | 4/28/2013 | on 15-day DL | Strained right oblique |
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| Francisco Cervelli | C | 4/27/2013 | on 60-day DL | Fractured right hand |
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| Ivan Nova | P | 4/27/2013 | on 15-day DL | Right triceps inflammation |
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| Cesar Cabral | P | 3/26/2013 | on 60-day DL | Left elbow pain |
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| Derek Jeter | SS | 3/22/2013 | on 60-day DL | Recovery from left ankle surgery |
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| Mark Teixeira | 1B | 3/22/2013 | on 60-day DL | Strained right wrist - out 8-10 weeks |
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| Michael Pineda | P | 3/16/2013 | on 60-day DL | Recovery from right shoulder surgery |
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| Alex Rodriguez | 3B | 2/13/2013 | on 60-day DL | Left hip surgery - out 4-6 months |
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