The aim of this study was to assess the effects of intensive training on menstrual function and related serum hormones and peptides.Forty female participants who attended a training course for an officer at the Korea Third Military Academy, and had regular menstrual periods were enrolled. Menstrual questionnaires and fasting blood samples were collected before entry and at 4-week intervals for 8 weeks. The levels of corticotropin-releasing hormone (CRH), cortisol, prolactin, endorphin-β, neuropeptide Y (NPY), leptin, orexin-A, ghrelin, follicle-stimulating hormone (FSH), luteinizing hormone (LH), estradiol (E2), thyrotropin (TSH), and thyroxine (T4) were determined.Body mass index and waist circumference decreased during the training course. Intensive training of military cadets resulted in changes of menstruation and related biomarkers. The levels of CRH, endorphin-β, NPY, orexin-A, ghrelin, E2, and T4 decreased substantially, and cortisol, prolactin, and TSH increased. Seventy percent of participants with regular menstrual periods before developed irregular during the training course. Participants were then categorized into 2 groups: those with regular menstruation (n = 12) and those with irregular menstruation (n = 28). The levels of hormones and peptides were not different between the 2 groups.In conclusion, cortisol, prolactin, and TSH level increased but levels of CRH, endorphin-β, NPY, orexin-A, ghrelin, E2, and T4 decreased throughout the training. Moreover, the levels were not different between participants with normal menstruation and those with irregular menstruation. Further research should extend these findings by investigating the exact mechanism by which high exercise levels, including intensive training, interfere with regular menstruation.