Abstract Objectives: To determine the inter-rater repeatability of a musculoskeletal examination and to compare findings between adolescent athletes and non-athletes in Finland. Methods: In this cross-sectional study, a musculoskeletal examination assessing posture, mobility and movement control was carried out by a sports and exercise medicine physician on 399 athletes aged 14–17 years and 177 non-athletes. Within 2 weeks another sports and exercise medicine physician repeated the examination for 41 adolescents to test the inter-rater repeatability. Results: In total, 10 of the 11 tests performed had at least moderate inter-rater reliability (κ ≥0.4 or percentage agreement >80%). Athletes more often than non-athletes had one shoulder protruded (8.0% vs 4.0%, OR 2.81, 95% CI 1.16 to 6.81). Forty-six per cent of athletes had good knee control in the two-legged vertical drop jump test compared with 32% of non-athletes (OR 1.99, 95% CI 1.29 to 3.06). Athletes had better core muscle control with 86.3% being able to remain in the correct plank position for 30 s compared with 68.6% of non-athletes (OR 2.70, 95% CI 1.67 to 4.36). In the deep squat test, good lumbar spine control was maintained only by 35.8% of athletes and 38.4% of non-athletes. Conclusions: A basic musculoskeletal examination is sufficiently reliable to be performed by trained physicians as a part of a periodic health evaluation. Shortfalls in mobility, posture and movement control are common in both athletes and non-athletes. These deficits could have been caused by sedentary behaviour, monotonous training, or both.