Practitioners often pay close attention to the effect of circadian, diurnal and ultra-dian rhythms on exercise and health in athletes. However, in female athletes, the menstrual cycle, which is an infradian rhythm, is sometimes overlooked. This chapter presents a systematic framework for working with female athletes by providing insight into the implementation and interpretation of screening and monitoring tools. The fluctuations in sex hormones can be altered by pregnancy, by chronological age and through the use of hormonal contraceptives. The screening process will also highlight the potential need for, and focus of, education, in addition to identifying the best form(s) of monitoring. Monitoring day-to-day physical, physiological and psychological changes across the menstrual cycle can provide insight into menstrual health and identify any potential perturbations. Due to large intra- and inter-variability in the menstrual cycle and the common use of hormonal contraceptives, the screening and monitoring tools and subsequent interpretation must be tailored to the individual.