Background: Knee pain is a common problem in children and adolescents, and it often has a chronic character. Purpose: To examine the prevalence of knee pain in 13-year-old children and assess associations of knee pain with physical factors and the presence of structural abnormalities on magnetic resonance imaging (MRI). Study Design: Cross-sectional study; Level of evidence, 3. Methods: Data from the Generation R Study, a population-based birth cohort, were used. Prevalence and characteristics of knee pain were assessed, using a pain mannequin, in children 13 years of age (N = 1849). Patient characteristics and data on physical activity were extracted from questionnaires. The body mass index standard deviation score and waist-hip ratio were calculated from objectively measured weight and height. Structural abnormalities were assessed by MRI. The differences between children with and without knee pain were also analyzed. Results: A prevalence of 8.0% was found for knee pain in children, of which 92.3% persisted for >3 months (ie, chronic); 37.5% of the children experienced pain daily, and the pain was almost always located on the anterior side of the knee (98.6%). Higher body mass index standard deviation scores were seen in children with knee pain than in the children without knee pain. No differences in physical activity were seen between children with and without knee pain. Moreover, in children with knee pain compared with children without knee pain, characteristics of Osgood-Schlatter disease (6.8% vs 1.9%) and bipartite patella type 3 (4.7% vs 0.3%) were more often seen on MRI. Conclusion: This study shows that knee pain is a relatively frequent problem in children. It is almost always located on the anterior aspect, has a chronic character, and is often experienced daily. However, the possible implication of structural abnormalities on MRI in children with knee pain and the possible relationship with the development of future knee complaints are still unclear.