ObjectiveChildren with special health care needs (SHCN) due to a chronic health condition perform more poorly at school compared to their classmates. There is still little knowledge on the causal pathways and which factors could be targeted by interventions. We, therefore, investigated school absenteeism in children with SHCN compared to their peers.MethodsThis study was based on data from the German population-based prospective cohort study ikidS (German for: I will start school). Children with SHCN were identified by the Children with Special Health Care Needs screener that captures five consequences of physical or mental chronic health conditions: (1) use or need of prescription medication, (2) above average use or need of medical, mental health, or educational services, (3) functional limitations compared with others of the same age, (4) use or need of specialized therapies, and (5) treatment or counseling for emotional, behavioral, or developmental problems. School absenteeism was defined as days absent from school due to illness during first grade and was reported by classroom teachers. Associations between SHCN consequences and school absenteeism were investigated by negative binomial regression models. Effect estimates were adjusted for confounding variables identified by a causal framework and directed acyclic graphs.Results1,921 children (mean age at follow-up 7.3 years, standard deviation 0.3; 49% females) were included; of these, 14% had SHCN. Compared to their classmates, children with SHCN had more days absent (adjusted rate ratio: 1.37; 95% confidence interval 1.16, 1.62). The effect was strongest among children with i) functional limitations, ii) treatment or counseling for emotional, behavioral, or developmental problems, and iii) those who experienced two or more SHCN consequences.ConclusionsChildren with SHCN have higher school absenteeism, which could–at least partly–explain their poorer school performance and lower educational attainment. SHCN-specific targeted interventions may reduce the adverse effects of SHCN on educational outcomes in children.