Background A thorough knowledge of the epidemiology and severity of injuries and illness in youth female elite sports is lacking due to the methodological challenges involved in recording them. In this study, the prevalence and incidence of injuries and illness are assessed among youth female elite athletes. Instead of solely focusing on time-loss injuries, our study included all substantial and non-substantial health problems (ie, injuries, mental problems and illnesses). Methods Sixty young elite Dutch female athletes (age: 16.6 years (SD: 2.3), weight: 58.3 kg (SD: 15.1), height: 154.1 cm (SD: 44.2)) participating in soccer (n=23), basketball (n=22) and gymnastic (n=15) talent development programmes were prospectively followed during one season (September 2014 to April 2015). To collect health problem data, all athletes completed the Oslo Sports Trauma Research Center Questionnaire on Health Problems every other week. Main outcome measures were average prevalence of injury and incidence density of injury. Results At any given time, 47.9% of the athletes reported an injury (95% CI 43.6% to 52.6%) and 9.1% reported an illness (95% CI 5.1 to 19.0). The average injury incidence density was 8.6 per 1000 hours of athlete exposure. The average number of self-reported injuries per athlete per season was significantly higher in soccer athletes (4.3±2.7) than in basketball athletes (2.6±2.0) (p=0.03) and not significantly higher than in the gymnastic squad. The knee and the ankle were two of the most common injury locations for all squads. Knee injuries in basketball and soccer and heel injuries in the gymnastic squad had the highest impact on sports participation. Conclusion High prevalence of self-reported injuries among talented female athletes suggests that future efforts towards their prevention are warranted.