PURPOSE: To determine whether changes in menstruation develop in female trainees during BCT and whether changes in body mass, body composition and/or physical activity are associated with menstrual interruption during BCT. METHODS: Female trainees grouped according to self-reported menstrual status in the 12 months before BCT as having regular cycles (RC; n = 352) or MD ( n = 97) completed height, body mass, and body composition assessments and questionnaires before and after BCT. Fisher's exact test and Mann-Whitney U test were used to compare between-group differences in categorical and continuous variables, respectively. Among RC trainees, odds ratios were calculated to examine the influence of changes in body mass, lean mass, and fat mass on a trainee's likelihood to miss a period during BCT. RESULTS: There were no differences in race, height, body mass, body mass index, or physical activity history at pre-BCT between RC and MD ( P > 0.05). Overall, 86% of trainees experienced changes to menstruation during BCT. RC were more likely than MD to have at least one period during BCT (81% vs 69%, respectively, P = 0.01). Among RC, gaining more body mass and lean mass and losing less fat mass were associated with increased odds of missing a period during BCT. CONCLUSIONS: These findings demonstrate that most female trainees experience menstrual changes during BCT. Menstrual cycle interruptions do not appear to align with loss of body or fat mass.