Throwing arm injuries are common because of the demand on the shoulder. Shoulder exams and pitching mechanics are regularly monitored by team physicians. Excessive instability and joint loading in baseball pitching are risk factors for throwing arm injuries. Altering baseball pitching mechanics affects both performance and the risk of injury. There is limited work on the relationship between shoulder exams, baseball pitching biomechanics, and their relationship with injury. Knowledge of the relationship between shoulder exam variables, baseball pitching mechanics, and injuries may provide new insights for treatments and rehabilitation protocols and improve performance. The purpose of this study is to investigate the relationship among injuries, shoulder exam variables, and pitching biomechanics in collegiate baseball pitchers. Pitching biomechanics, shoulder exam tests, and self-reported injury questionnaires from 177 collegiate baseball pitchers were used in this study. The study protocol was approved by an institutional board, and all participants gave written informed consent. Pitching motion data was collected at 240 Hz using a motion capture system. A custom program was used to calculate all kinematic and kinetic variables of baseball pitching. The shoulder range of motion and flexibility were quantitatively recorded using a custom-made wireless device. Self-reported injury questionnaires were filled out during testing and during yearly follow-ups. All subjects with injuries were divided into three groups: injury history, follow-up injury, and both injury history and follow-up injury. All pitchers were healthy at the time of testing. Analysis of variance with Tukey post-hoc tests, Pearson correlation tests, and multinomial logistic regression tests were performed using SPSS to compare differences among shoulder exam, pitching biomechanics, and injury questionnaire variables with alpha set to 0.05. When comparing shoulder exam variables to pitching biomechanics there were 34 positive and 21 negative significant correlations (positive R: 0.230 to 0.356 and negative R: -0.203 to -0.245, respectively). When comparing shoulder exam variables to injuries there was a significant difference in the dominant internal shoulder rotational flexibility among the three injury groups (p=0.026). There was a significant difference in the shoulder horizontal adduction angle among the three injury groups (p=0.045). A throwing biomechanics index was created finding fifteen significant pitching biomechanics variables related to injury. The throwing biomechanics index found significant relationships with the pitcher’s height (p=0.017), mass (p=0.000), age (p=0.010), forearm length (p=0.000), shoulder flexibility (p=0.002), and shoulder range of motion (p=0.010). Our findings show that the shoulder exam, pitching biomechanics, and injury questionnaire variables are related. Optimizing pitching mechanics and shoulder flexibility reduces injury and improve performance. Pitching mechanics consists of kinematics and kinetics and improvement is found when pitching with proper mechanics. Shoulder flexibility is improved by proper strengthening and conditioning. The throwing biomechanics index’s relationship with both demographics and the shoulder exam shows that the single index is representative and can lead to new insights. The ability to understand the relationship between shoulder exam variables, baseball pitching mechanics (motions and joint loadings), and injuries helps further our knowledge and pushes forward the underlying goal of this study which is to improve performance and reduce injuries.