Introduction: Compared to typically developing peers, children with disabilities due to neurodevelopmental disorders and disabilities (NDD/D) and to chronic medical conditions (CMC) have reduced participation in activities. The extent to which these two groups of children have different levels of participation is unknown and was examined in this study. Methods: The 2006 Participation and Activity Limitation Survey children dataset collected by Statistics Canada was analyzed. Children with disabilities due to NDD/D and CMC were identified following review and classification of all ICD-10 codes in the dataset by two pediatricians. Dependent variables were parent-reported child participation in supervised and unsupervised physical activities within and outside of school, educational activities, and social/recreational activities. Logistic regression analyses, with relevant covariates (child and familial characteristics), were used to analyze the data. Results: Children with NDD/D were significantly more likely to take part in supervised and unsupervised physical activity at school than children with CMC (p less than 0.001). A similar trend was observed for participation in school outings, although the effect was not significant at p less than 0.01. Finally, a trend in the opposite direction was observed for educational activities, as children with NDD/D were less likely to take part in these activities than children with CMC. Discussion: Finding decreased participation among children with CMC compared with NDD/D was not predicted a priori but has potential implications for their mental and physical health. Conclusions: Gaining a better understanding of the barriers to participation in physical activity may contribute to improving the overall health status of children with CMC. (Contains 3 tables.)