Background: Autism spectrum disorder (ASD) and intellectual disability (ID) affect 2-3% of the global population with both conditions having unclear pathophysiology. Little data exists from South Asia examining the association between these conditions and the disturbances in thyroid profile and vitamin-D status. Objective: This study sought to characterize the association between these conditions and serum thyroid-stimulating hormone (TSH) and 25-hydroxycholecalciferol (25(OH)D3) levels, from a resource-limited setting in India. Methods: The present work was a prospective case-control study conducted and reported in accordance with Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) guidelines. Children with ASD, children with ID, and age-and-sex matched healthy controls, attending the outpatient clinics of pediatrics and psychiatry in Northern India were included. Primary outcomes were serum TSH and 25(OH)D3 levels, which were measured by chemiluminescent immunoassay and compared using ANOVA. Results: A total of 75 children were included, of which 15 had ASD, 30 with ID, and 30 were controls. There were 44 males and 31 females, with a mean age of 7.01±2.77 years. Mean±SD levels of 25(OH)D3 were significantly lower in ASD (9.53±4.93 IU/mL) and ID (14.39±5.99 IU/mL) compared to healthy controls (16.37±10.68 IU/mL) [p=0.032]. Mean±SD levels of TSH were similar in ASD (2.65±1.96), ID (2.47±2.03), and controls (2.19±1.42), with no significant difference [F-value=0.37; P=0.69]. 8% (N=6/75) of the participants had a raised TSH level. Conclusion: Children with ASD and ID have significantly lower vitamin D3 levels compared to healthy controls. High-quality randomized controlled trials are warranted to further investigate the therapeutic impact of early-life vitamin D supplementation in these indications.