Musculoskeletal (MSK) pain is frequently reported among adolescents and children and a common reason for consultation in primary care. Our aim is to examine its prevalence in 6-year old children in a general population and to assess associations with physical and psychosocial factors. Data from the Generation R Study, a population based cohort, was used. Prevalence and characteristics of MSK pain were assessed with parent-reported questionnaires at 6-years of age (N=6200). Demographics and data on physical activity, sedentary behaviors, previous reported MSK pain and behavioral problems were extracted from questionnaires. The BMI SD score was calculated from objectively measured weight and height. A three-month prevalence of 10.0% was found for MSK pain in children, of which one third was chronic, and 44.6% experienced together with pain at other sites. Univariate analyses showed that boys and children with lower socioeconomic status (SES) reported MSK pain more frequent compared to other pain and no pain. While no associations were found between MSK pain and children's BMI and physical activity level, children with MSK pain were more likely to watch television ≥2 hours/day. Multivariable analysis showed significant associations for MSK pain at 3 years of age (OR 5.10, 95% CI 3.25 to 7.98) and behavioral problems (OR 2.10, 95% CI 1.19 to 3.72) with the presence of MSK pain. So, MSK pain is already common in young children and is often chronic or recurrent. Previous reported MSK pain and behavioral problems are independently associated with MSK pain in the studied population.