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Several studies have suggested an association between vitamin D in childhood and autism spectrum disorder. No prospective studies have evaluated whether lower vitamin D levels precede ASD diagnoses -- a necessary condition for causality. The objective of this study was to prospectively evaluate whether vitamin D serum levels in early childhood was associated with incident physician diagnosed ASD. A prospective cohort study was conducted using data from preschool-aged children in the TARGet Kids! practice-based research network in Toronto, Canada, from June 2008 to July 2015. 25-hydroxyvitamin D concentration was measured through blood samples and vitamin D supplementation from parent report. Autism spectrum disorder diagnosis was determined from medical records at follow-up visits. Covariates included age, sex, family history of autism spectrum disorder, maternal ethnicity, and neighborhood household income. Unadjusted and adjusted relative risks and 95% confidence intervals were estimated using Poisson regression with a robust error variance. In this study, 3852 children were included. Autism spectrum disorder diagnosis was identified in 41 children (incidence = 1.1%) over the observation period (average follow-up time = 2.5 years). An association between 25-hydroxyvitamin D concentration and autism spectrum disorder was not identified in the unadjusted (relative risk = 1.04, 95% confidence interval: 0.97, 1.11 per 10 nmol/L increase in 25-hydroxyvitamin D concentration) or adjusted models (adjusted relative risk = 1.06; 95% confidence interval: 0.95, 1.18). An association between vitamin D supplementation in early childhood and autism spectrum disorder was also not identified (adjusted relative risk = 0.86, 95% confidence interval: 0.46, 1.62). Vitamin D in early childhood may not be associated with incident physician diagnoses of autism spectrum disorder.