Abstract Background The child's lower limb is the most commonly reported musculoskeletal location with pain and also the most commonly injured site in sports. Some potential risk factors have been studied, but the results are inconsistent. We hypothesized that distinction of traumatic from non-traumatic pain would provide a clearer picture of these factors. The aim of this study is to assess factors associated with lower extremity pain and its impact on preadolescents in a population-based cohort. Methods A structured pain questionnaire was completed by 1756 schoolchildren of third and fifth grades to assess musculoskeletal pain, psychosomatic symptoms, subjective disabilities, school absence and frequency of exercise. In addition, hypermobility and physical fitness were measured. Results The knee was the most common site of pain followed by the ankle-foot and thigh. Of the children who reported pain in their lower extremity, approximately 70% reported at least one disability and 19 % reported school absence attributed to their pain during the previous three-month period. Children with traumatic pain had a higher subjective disability index than those with non-traumatic pain (P = 0.02). Age less than 11 years, headache, abdominal pain, depressive feelings, day tiredness, and vigorous exercise were more common in children with lower limb pain than those free of it. In the stratified analysis, younger age was related to both traumatic and non-traumatic pain groups. Vigorous exercise was positively associated with traumatic pain, while subjects with non-traumatic pain had more frequent psychosomatic symptoms. Conclusion Risk factors and consequences of traumatic and non-traumatic lower limb pain are not similar. Traumatic lower limb pain is associated with practicing vigorous exercise and high level of physical fitness, while non-traumatic pain is more correlated with psychosomatic symptoms. These differences might be one of the reasons for the discrepancy of previous research conclusions. The two conditions need to be treated as different disorders in future studies.