Exercise-associated benefits on the cardiovascular systems are well established. Although exercise-associated sudden cardiac death is rare, most deaths in young athletes are due to hereditary or congenital cardiac diseases. Athletic adaptation itself is associated with several structural changes that overlap those observed in individuals with cardiomyopathies, often leading to dilemmas for the clinician regarding life-changing decisions including advice against competitive sports participation. Cardiac magnetic resonance plays an increasingly important role in helping to establish an accurate diagnosis in these individuals. This review highlights the role of cardiac magnetic resonance in differentiating physiological adaptation in athletes from pathology.