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Objectives Declining physical fitness, rising obesity and mental and behavioural diagnoses are growing public health issues in young adults. This study aimed to examine the associations between cardiorespiratory and muscular fitness and waist circumference with mental and behavioural diagnoses in a large, population-based sample of young men.Methods We performed a retrospective cohort analysis using data from the Finnish Defence Forces. Cardiorespiratory fitness (12 min running test), muscular fitness (muscular fitness index combining push-ups, sit-ups and standing long jump) and waist circumference were measured at the beginning of compulsory military service. These data were linked with physician-diagnosed mental and behavioural diagnoses (International Classification of Diseases, 10th Revision F-diagnoses) in individuals who interrupted their service. The sample consisted of 156 202 men (mean age 19.7 years), representing over two-thirds of the national male age cohort.Results In total, 4034 men interrupted service due to mental and behavioural diagnoses. These individuals had lower levels of cardiorespiratory fitness (2250±390 m vs 2410±380 m, p<0.001) and muscular fitness index scores (10.4±2.5 vs 11.2±2.7, p<0.001) than those who completed their military service. After adjusting for age, body mass index and year of the service, lower cardiorespiratory fitness (OR 0.88, 95% CI 0.88 to 0.89) and muscular fitness (OR 0.88, 95% CI 0.86 to 0.89) remained significantly associated with service interruption. Greater waist circumference showed no general association, except in cases of hyperkinetic disorders.Conclusions Among young men, lower levels of cardiorespiratory and muscular fitness are universally associated with mental and behavioural diagnoses during military service. Co-occurrence between physical fitness and mental and behavioural diagnoses suggests that good physical fitness may be an important component of overall mental health in this population.