Overweight and obesity have been reported to be more prevalent in populations with autism spectrum disorder than in children with typical development. The aim of this study was to compare the anthropometric status of children with autism spectrum disorder (diagnosed and subclinical) and children with typical development and analyse which variables can affect the anthropometric and health status of children with autism spectrum disorder. We present a two-phase epidemiological study in a school population of two age groups which assesses autism spectrum disorder diagnosis, anthropometric data and bioelectrical impedance analysis. From an initial sample of 3,713 children, 79 with autism spectrum disorder, 42 with subclinical autism spectrum disorder and 350 with typical development participated in the study. Pre-schoolers with autism spectrum disorder were taller than pre-schoolers with typical development. School-age children with autism spectrum disorder showed a significantly higher body mass index and rate of overweight/obesity than children with typical development (63.4% vs 46.3%). No significant differences were found for bioelectrical impedance analysis, but school-age children with autism spectrum disorder showed a significantly higher waist circumference, waist/height ratio and cardiovascular risk than children with typical development. The quality of the diet was lower in children with autism spectrum disorder than in children with typical development. Multiple regression analyses showed that having autism spectrum disorder and internalizing psychological problems were associated with waist/height ratio and high cardiovascular risk in school-age children.