Magnetic resonance (MR) imaging is important in diagnosing musculoskeletal injuries in horses. However, there is still much to learn regarding the significance of lesions identified in equine MR images. Of particular importance is the clinical significance of signal change as a function of pulse sequence. We hypothesized that a resolution of tendon, ligament, and bone marrow lesions on short-tau inversion recovery (STIR) images would be associated with a return to soundness, and that a persistence of tendon and ligament lesions on only T1-weighted (T1w) gradient recalled echo (GRE) images would not be associated with persistent lameness. The medical records and MR images of 27 horses that had a hyperintense lesion in initial STIR MR images followed by a subsequent follow-up MR imaging examination were reviewed. Horses whose tendon or ligament lesions had resolved on STIR images at the time of the recheck examination were significantly more likely to be sound than horses whose lesions persisted on STIR images (P=0.039). This association did not exist in horses with bone marrow lesions (P=1.00). Horses whose tendon or ligament lesions persisted only on T1w GRE images were no more likely to be sound than horses whose lesion persisted on at least one other sequence type (P=0.26). However, the low number of horses included in this analysis may have precluded identification of a significant difference in lameness status. Tendon or ligament lesions visualized on STIR images may represent active lesions that may contribute to lameness in the horse.