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Background: Shoulder pain is the most common and well-documented site of musculoskeletal pain in elite swimmers. Structural abnormalities on magnetic resonance imaging (MRI) of elite swimmers’ symptomatic shoulders are common. Little has been documented about the association between MRI findings in the asymptomatic shoulder versus the symptomatic shoulder. Objective: To assess clinically relevant MRI findings in the shoulders of symptomatic and asymptomatic elite swimmers. Method: Twenty (aged 16–23 years) elite swimmers completed questionnaires on their swimming training, pain and shoulder function. MRI of both shoulders (n = 40) were performed and all swimmers were given a standardised clinical shoulder examination. Results: Both shoulders of 11 male and 9 female elite swimmers (n = 40) were examined. Eleven of the 40 shoulders were clinically symptomatic and 29 were asymptomatic. The most common clinical finding in both the symptomatic and asymptomatic shoulders was impingement during internal rotation, with impingement in 54.5% of the symptomatic shoulders and in 31.0% of the asymptomatic shoulders. The most common MRI findings in the symptomatic and asymptomatic shoulders were supraspinatus tendinosis (45.5% vs. 20.7%), subacromial subdeltoid fluid (45.5% vs. 34.5%), increased signal in the AC Joint (45.5% vs. 37.9%) and AC joint arthrosis (36.4% vs. 34.5%). Thirty-nine (97.5%) of the shoulders showed abnormal MRI features. Conclusion: MRI findings in the symptomatic and asymptomatic shoulders of young elite swimmers are similar and care should be taken when reporting shoulder MRIs in these athletes. Asymptomatic shoulders demonstrate manifold MRI abnormalities that may be radiologically significant but appear not to be clinically significant.