The objective of this paper was to determine the cost effectiveness of exercise therapy (intervention group) compared with "usual care" (control group) in adolescents and young adults with the patellofemoral pain syndrome in primary care. This multicenter prospective randomized clinical trial with cost-utility analysis was conducted at 38 general practices and three sport medical advice centers in the Netherlands for 2007. A total of 131 patients were included. The annual direct medical costs per patient were significantly higher for the intervention group (euro 434) compared with the control group (euro 299) mainly caused by additional physiotherapy visits. The average annual societal costs per patient were significantly lower in the intervention group (euro 1011 vs euro 1.166). Productivity costs were the largest cost component, in particular costs due to reduced efficiency at paid work which were responsible for 47% and 56% of the total costs in the intervention and control group respectively. Patients in the intervention group experienced a slightly, but not significantly, higher quality of life (0.8722 vs 0.8617). With a cost effectiveness ratio of -euro 14,738 per quality adjusted life year, exercise therapy appears to be cost effective as compared with "usual care."