Introduction: Non-combat musculoskeletal injuries (MSKIs) during military training significantly impede the US military's functionality, with an annual cost exceeding $3.7 billion. This study aimed to investigate the effectiveness of a markerless motion capture system and full-body biomechanical movement pattern assessments to predict MSKI risk among military trainees. Methods: A total of 156 male United States Air Force (USAF) airmen were screened using a validated markerless biomechanics system. Trainees performed multiple functional movements, and the resultant data underwent Principal Component Analysis and Uniform Manifold And Projection to reduce the dimensionality of the time-dependent data. Two approaches, semi-supervised and supervised, were then used to identify at-risk trainees. Results: The semi-supervised analysis highlighted two major clusters with trainees in the high-risk cluster having a nearly five times greater risk of MSKI compared to those in the low-risk cluster. In the supervised approach, an AUC of 0.74 was produced when predicting MSKI in a leave-one-out analysis. Discussion: The application of markerless motion capture systems to measure an individual's kinematic profile shows potential in identifying MSKI risk. This approach offers a novel way to proactively address one of the largest non-combat burdens on the US military. Further refinement and wider-scale implementation of these techniques could bring about substantial reductions in MSKI occurrence and the associated economic costs.