Limited information exists regarding the association between distal interphalangeal joint (DIPJ) abnormalities with changes of the synovial invaginations of the distal sesamoid (navicular) bone. This retrospective study measured specific characteristics of the synovial invaginations of the navicular bone to determine whether any single characteristic was associated with abnormalities in the DIPJ or navicular apparatus (NA), using high field MRI. The DIPJ and NA were graded independently by three scorers, and the grades then averaged, creating a global pathology score for the DIPJ, NA, and synovial invaginations, using 200 scans of horses' feet. Higher global scores represented more severe pathology. The number of invaginations, depth of penetration, invagination shape, and cross sectional area (CSA) of the largest invagination were recorded. Interobserver agreement was measured using Cohen’s Kappa. Associations of global scores of the DIPJ and NA with individual invagination characteristics were assessed using linear mixed modeling. A significant relationship was found between the number of invaginations and global DIPJ score, with higher invagination numbers associated with higher DIPJ scores. For invagination depth and CSA, a significant relationship was noted with global scores of both the DIPJ and NA. Reliable relationships between shapes of synovial invaginations and global scores of DIPJ and NA were not found, likely due to poor interobserver scoring (0.305). These findings suggest that primary DIPJ disease and NA pathology should be considered when noticing alterations to navicular synovial invaginations on MRI. This contrasts traditional views that synovial invagination abnormalities are indicative solely of NA pathology.