Background: Musculoskeletal disorders are common among military personnel, especially during the initial basic training period. Prior studies have reported the prevalence rate of overall musculoskeletal symptoms or injuries in different military population and nationalities, especially from North America and Europe; however, very limited information regarding the military population of South America exists. Although Brazil has one of the biggest military forces worldwide (���335,000 military personnel), currently, to our knowledge, there is no study reporting musculoskeletal symptoms or injury statistics in the Brazilian Armed Forces. Thus, the aims of this study were to describe the 12-month prevalence rate of self-reported musculoskeletal symptoms in cadets and to compare this prevalence rate between sexes and school years. Methods: We conducted a cross-sectional study that took place from January to March 2016. Participants were Navy cadets, of both sexes and from three different school years of a Brazilian Merchant Navy Academy. All volunteers completed an adapted version of the Brazilian Nordic Musculoskeletal Questionnaire that assessed the past 12-month prevalence of musculoskeletal symptoms over eight body regions of the trunk and lower extremity. The Pearson���s �� 2 test was conducted to compare prevalence of symptoms per body region between sexes and among the 3 school years. The study has been approved by the Naval Hospital���s ethical committee. Results: A total of 545 cadets (394 males), corresponding to 79% of all 688 cadets enrolled at the Merchant Navy Academy, volunteered to participate on this study. Among all cadets, 266 (49%) reported symptoms in at least one body region in the past 12-months. The knee with 116 (21%) and lower back with 96 (18%), were the most prevalent regions. In terms of sex differences, there was higher prevalence of symptoms among females 90 (60%) than males 176 (45%). Furthermore, females reported almost double the prevalence for lower back symptoms (27% vs. 14%, p = 0.001) and 11% higher prevalence of knee symptoms (29% vs. 18%, p = 0.006) than males. Finally, it is important to highlight that cadets from the second (127 [65%]) and third (77 [55%]) school years had higher prevalence of symptoms than cadets from the first year (62 [29%]). The knee and lower back were consistently the two most prevalent regions among all school years, but shin symptoms increased from 3% to 17% (p < 0.001) between the first and second school years. Conclusion: 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.