Triathlon is a popular sport for both recreational and competitive athletes. This study investigated the rates and patterns of stress fractures in the German national triathlon squad. We developed a web-based retrospective questionnaire containing questions about the frequency of stress fractures, anatomic localisation and associated risk factors. The survey was conducted as an explorative cross-sectional study. Eighty-six athletes completed the questionnaire. Twenty athletes (23%) sustained at least one stress fracture. All documented stress fractures were located in the lower extremities. Factors associated with a higher risk for stress fractures were female gender, competitive sport prior to triathlon career, Vitamin D or iron deficiency, menstrual disturbances and a high number of annual training hours. Disseminating knowledge among athletes and their professional community in order to raise awareness about early symptoms and relevant risk factors could help to improve prevention and reduce the incidence of stress fractures.