Musculoskeletal pain is common in children but studies on the outcome and predictive factors for persistence/recurrence of these symptoms are scarce. A baseline cross-sectional survey of 1,756 schoolchildren (mean age 10.8) identified 564 (32.1%) children with musculoskeletal pain. At baseline, these children were evaluated using a structured questionnaire and examined for hypermobility and physical fitness. The children were re-evaluated after one year, and four years (at adolescence) using the same pain questionnaire. At 1-year follow-up, 53.8% (95% CI 48.8-58.8) of the children reported pain persistence (persistent preadolescent musculoskeletal pain). At 4-year follow-up, 63.5% (95% CI 58.7-68.1) of them had musculoskeletal pain. Neck was the site with most persistent/recurrent musculoskeletal pain. Those with persistent preadolescent musculoskeletal pain had approximately three times higher risk of pain recurrence (OR=2.90 [95% CI 1.9-4.4]). In the univariate analysis, female gender, older age group (11+), hypermobility, co-existence of psychosomatic symptoms, having high disability index, and reporting combined musculoskeletal pain at baseline predicted pain recurrence at adolescence. In the multivariate analysis, age, headache, hypermobility and having combined musculoskeletal pain were found as independent predictors. Statistically significant sex interactions were found for age, depressive feelings, waking up during nights and hypermobility. More psychosomatic symptoms predicted pain recurrence in girls than in boys, and hypermobility was a strong predictor in females only. Musculoskeletal pain in preadolescents is not a self-limiting phenomenon and more studies are still warranted to explore its determinants aiming to improve the long-term outcome of these symptoms.