Background Somatic symptoms among adolescents are common, yet little is known about long-term trajectories of somatic symptoms and the factors in adolescence that shape them. We examined individual, family and school-based factors at age 16 as predictors of trajectories of somatic symptoms over 27 years. Methods Participants from the Northern Swedish Cohort (n = 1001) responded to questions about individual factors (e.g. health behaviours), family factors (e.g. contact with parents, social and material adversity) and school satisfaction at age 16; as well as 10 somatic symptoms at ages 16, 18, 21, 30 and 43. Teacher assessments at age 16 included overall ability at school and peer relations. Age 16 predictors of somatic symptom trajectory group membership were analysed using multinomial logistic regression. Results Poor contact with mother and poor school satisfaction were significant predictors of adverse symptom trajectories among both men and women. Low birth weight and low parental academic involvement were contributing factors for women, while smoking and social adversity were more relevant factors for men. Conclusions Our findings emphasize the importance of a holistic approach that considers the unique contributions of individual, family and school-based factors in the development of trajectories of somatic symptoms from adolescence to middle age.