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The prevalence of musculoskeletal symptoms in the Brazilian Merchant Navy Academy doubles between initial enrollment and the beginning of the second school year. Females have consistently higher rates of symptoms than males, particularly reporting higher prevalence of knee and lower back pain which are the two most prevalent regions in this population. Prevention efforts should concentrate on the basic training period in an attempt to decrease the prevalence of musculoskeletal symptoms in this population. Finally, prospective studies are required to verify the cause and effect relationship between training and musculoskeletal symptoms.