Introduction: The adolescent years represent a key period for the development of musculoskeletal complaints (MSC) and the differences between boys and girls. We evaluated the prevalence and course of MSC and factors associated with MSC while growing up from age 11 to age 20. Methods: Questionnaire-based data at age 11 (n = 2,638), age 14 (n = 2,517), age 17 (n = 2,094) and at age 20 (n = 2,206) from the ongoing Prevention and Incidence of Asthma and Mite Allergy (PIAMA) birth cohort were analyzed. MSC refers to pain of lower back, upper- and/or lower extremities. A multivariable logistic regression analysis was used to evaluate a number of factors in relation to persistent pain (pain reported at three out of four measurements). Results: Prevalence of MSC increased from 14.2% at age 11 to 22.1% at age 20 for boys, and from 17.4% at age 11 to 37.9% at age 20 for girls. Persistent pain was found among 5.1% of the boys and 16.5% of the girls. Being bullied, sleeping problems and tiredness during the day were significantly associated with persistent pain, in both boys and girls, while the latter two were more prevalent among girls. Self-reported (sports-) accidents, and among girls also early onset of puberty, were also significantly associated with persistent pain, but lifestyle factors, such as physical activity and smoking, were not. Conclusion: The prevalence of MSC increases during adolescence, with a widening gap between boys and girls. The factors associated with MSC are similar in boys and girls, though the prevalence of some of these differ by sex. Significance: Measuring a group of youngsters 4 times between age 11 and 20 shows an increase in the percentage reporting musculoskeletal complaints (MSC) with a widening gap between girls and boys, with more pain among girls. Boys and girls do hardly differ with respect to factors associated with MSC, being mainly psychosocial factors and (sports) accidents.