Purpose: Currently, caries risk assessment tools consider all children with special health care needs (CSHCN) in tandem; we tested this notion by examining caries risk among and within four distinct CSHCN groups: Autism (ASD), Congenital Heart Disease (CHD), Cerebral Palsy (CP); Down Syndrome (DS); and a control (healthy) group. Methods: We assembled a retrospective longitudinal cohort of 150 patients (30 in each group) of a private pediatric dental practice and extracted information on caries diagnoses and 21 postulated caries risk factors from clinical records. We used bivariate tests and multivariable Poisson regression modeling to estimate caries incidence rates (IR), ratios (IRRs) and 95% confidence intervals (CI). Results: CSHCN had higher caries burden and caries risk (IR=0.049 per person-year) compared to controls (IR=0.033). Caries risk was nearly double among CHD [IRR =1.9 (95% CI=0.72-5.2) vs. controls] compared to DS [IRR=1.04 (95% CI=0.38-2.9)]. 'Visible cavities or fillings' was the only significant caries risk factor, yet it did not alter the between-CSHCN group (i.e., CHD>DS, controls) caries risk heterogeneity. Conclusions: CSHCN is a heterogeneous group that must be treated in a precise, diagnosis-specific manner in caries risk assessment. Caries experience in the primary dentition was the only significant predictor of permanent dentition caries incidence.