Introduction: Osteoarthritis (OA) and rotator cuff tear (RCT) pathologies have distinct scapular morphologies that impact disease progression. Previous studies examined the correlation between scapular morphology and glenohumeral joint biomechanics through critical shoulder angle (CSA) variations. In abduction, higher CSAs, common in RCT patients, increase vertical shear force and rotator cuff activation, while lower CSAs, common in OA patients, are associated with higher compressive force. However, the impact of the complete patient-specific scapular morphology remains unexplored due to challenges in establishing personalized models.Methods: CT data of 48 OA patients and 55 RCT patients were collected. An automated pipeline customized the AnyBody (TM) model with patient-specific scapular morphology and glenohumeral joint geometry. Biomechanical simulations calculated glenohumeral joint forces and instability ratios (shear-to-compressive forces). Moment arms and torques of rotator cuff and deltoid muscles were analyzed for each patient-specific geometry.Results and discussion: This study confirms the increased instability ratio on the glenohumeral joint in RCT patients during abduction (mean maximum is 32.80% higher than that in OA), while OA patients exhibit a higher vertical instability ratio in flexion (mean maximum is 24.53% higher than that in RCT) due to the increased inferior vertical shear force. This study further shows lower total joint force in OA patients than that in RCT patients (mean maximum total force for the RCT group is 11.86% greater than that for the OA group), attributed to mechanically advantageous muscle moment arms. The findings highlight the significant impact of the glenohumeral joint center positioning on muscle moment arms and the total force generated. We propose that the RCT pathomechanism is related to force magnitude, while the OA pathomechanism is associated with the shear-to-compressive loading ratio. Overall, this research contributes to the understanding of the impact of the complete 3D scapular morphology of the individual on shoulder biomechanics.