Background: Anterior knee pain and intermittent low back pain are among the most common orthopedic complaints of adolescents. However, little is known about pes planus and its relative risk for these symptoms. The goal of the study was to track the prevalence of pes planus in adolescents, and examine its associated risk to anterior knee pain and intermittent low back pain, respectively. Materials and Methods: A retrospective study of 97,279 military recruits presenting to recruitment centers was conducted. Pes planus was graded by an orthopedist as mild, moderate or severe according to the flattening of the plantar arch and its rigidity to standing on one's toes. Anterior knee pain was diagnosed when symptoms were attributed to the patellofemoral joint. Intermittent low back pain was diagnosed when there was pain but neither abnormal clinical nor radiographic findings. Results: Pes planus was present in 15,698 (16%) individuals. 11,549 (74%), 3,341 (21%) and 808 (5%) were diagnosed as having mild, moderate and severe pes planus, respectively. The prevalence of intermittent low back pain was 5% in both the control and mild pes planus groups, while it was 10% in the moderate and severe pes planus groups (p < 0.0001). The prevalence of anterior knee pain was 4% in both the control and mild pes planus groups, while it was 7% in the moderate and severe pes planus groups (p < 0.0001). Conclusion: Moderate and severe pes planus was associated with nearly double the rate of anterior knee pain and intermittent low back pain, while mild pes planus was associated with no higher rate for these problems. Prophylactic measures may be helpful only in those adolescents with moderate and severe pes planus.