The purpose of this investigation was to determine the association between gender and the prevalence and incidence of patellofemoral pain syndrome (PFPS). One thousand five hundred and twenty-five participants from the United States Naval Academy (USNA) were followed for up to 2.5 years for the development of PFPS. Physicians and certified athletic trainers documented the cases of PFPS. PFPS was defined as retropatellar pain during at least two of the following activities: ascending/descending stairs, hopping/jogging, prolonged sitting, kneeling, and squatting, negative findings on examination of knee ligament, menisci, bursa, and synovial plica, and pain on palpation of either the patellar facets or femoral condyles. Poisson and logistic regressions were performed to determine the association between gender and the incidence and prevalence of PFPS, respectively. The incidence rate for PFPS was 22/1000 person-years. Females were 2.23 times (95% CI: 1.19, 4.20) more likely to develop PFPS compared with males. While not statistically significant, the prevalence of PFPS at study enrollment tended to be higher in females (15%) than in males (12%) (P=0.09). Females at the USNA are significantly more likely to develop PFPS than males. Additionally, at the time of admission to the academy, the prevalence of PFPS was not significantly different between genders.