A 2007 study by Dick et al in the Journal of Athletic Training looked at injury rates for the men's baseball using the NCAA injury surveillance system from 1988-2004.
45% of all injuries were to the upper extremity and about 30% were to the lower extremity. The most frequent game injuries were:
Upper leg strains (11%)
Ankle sprains (7.4%)
Shoulder strains (6.5%).
The most common practice injuries were:
Shoulder strains (10%)
Ankle sprain (8.5%)
Upper leg strain (8.3%)
Regarding mechanisms of injury, contact with something other than another player accounted for 45% of injuries while 42% of injuries were non-contact. For game injuries resulting in 10 or more days off, lower extremity injuries accounted for 19.7% followed by shoulder and elbow injuries at 4.3%. For practice, shoulder injuries were the major cause of significant time off. Of all shoulder and elbow injuries, pitching accounted for 73.0% and 78.4% respectively.
When looking at injuries by position:
General baseball rate of injury found in this study were 1.85 injuries per 1000 athlete-exposures (A-Es) for practices and 5.78 injuries per 1000 A-Es for games. This study showed that baseball had the lowest practice injury rate and the third lowest game injury rate compared with the other 14 sports for which injury data was collected through the NCAA surveillance system.
A 2011 study in the American Journal of Sports Medicine by Posner et al looked at Major League Baseball injuries from 2002-2008 using information obtained from the MLB disabled list since there is no injury surveillance system in place.
They found the general rate of injury was 3.61 per 1000 A-Es. Pitchers had 34% higher injury rate then fielders. Among all player injuries, upper extremity injuries accounted for 51.4%, while lower extremity injuries were 30.6%.