Cohort study. Shoulder pain prevalence is high in those with spinal cord injury (SCI) and is associated with decreased function, participation restrictions and decreased quality of life. Limited evidence exists regarding physical impairments of newly acquired SCI. The current study compared musculoskeletal factors at rehabilitation initiation in individuals with newly acquired SCI to uninjured individuals. We hypothesized no impairment differences of shoulder pain, strength, mobility, muscle extensibility, or rotator cuff integrity would exist between groups. Multi-site laboratory setting. Thirty-five individuals with newly acquired SCI and age and gender-matched controls without SCI (n = 34) participated. Musculoskeletal Pain Survey, shoulder range of motion (ROM), strength, pectoralis minor muscle extensibility (PM) and tissue integrity [Ultrasound Pathology Rating Scale (USPRS)] were obtained. Higher pain was reported by individuals experiencing new SCI along with lower strength across all bilateral measures, reduced elevation, external rotation, and horizontal adduction ROM, with large effect sizes. PM bilateral extensibility was reduced compared to controls, with moderate between group effect size; however, no USPRS score difference existed. This study provided the first comprehensive clinical description for individuals with newly acquired SCI. In comparison to matched uninjured controls, participants with new SCI reported greater shoulder pain with impairments in mobility, strength, and extensibility. The identified early clinical impairments aligned with progressive impairment including further pain development and persistence. Awareness and modification of these early clinical impairments may lead to improved long-term outcomes, improving the overall health and well-being of individuals with newly acquired SCI. Spinal Cord Injury Research Program Investigator-Initiated Research Award under Award No. W81XWH-17-1-0476.