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In female athletes, the reproductive system can be largely impacted by hormonal changes associated with exercise and energy balance. The female sex hormone estrogen has measurable effects on muscle function, tendon and ligament strength, and subsequently the musculoskeletal system.This study was designed to investigate the association between menstrual cycle status and musculoskeletal disorders (MsDs) among female athletes in Nigeria.A cross-sectional survey of female athletes at the National Stadium Abuja, Nigeria.Participants were selected using a purposive sampling technique. Bio-data forms, Menstrual History Questionnaires, and Nordic Musculoskeletal Questionnaires were used for data collection.There was a 24.9% prevalence of menstrual irregularities among participants, of which 15.4% and 9.5% reported oligomenorrhea and amenorrhoea, respectively. The overall 12-month prevalence of MsDs was 56.6%. Prevalence of MsDs among participants who self-reported menstrual irregularity was 81.1% and 69.6%, respectively, for oligomenorrhea and amenorrhea. A significant association (P = .001) existed between menstrual cycle status and MsDs among female athletes in Nigeria. Amenorrheic female athletes were found to have higher occurrences of missing participation in sports for more than 30 days due to major MsDs.Prevalence of menstrual irregularities was high among female athletes and is associated with MsDs.Physical therapists should educate female athletes on relationship between their menstrual status and their musculoskeletal health and sports performance.