Bone development, casein-free diet use, supplements, and medications were assessed for 75 boys with autism or autism spectrum disorder, ages 4–8 years. Second metacarpal bone cortical thickness (BCT), measured on hand-wrist radiographs, and % deviations in BCT from reference medians were derived. BCT increased with age, but % deviations evidenced a progressive fall-off (p = .02): +3.1 ± 4.7%, −6.5 ± 4.0%, −16.6 ± 3.4%, −19.4 ± 3.7%, −24.1 ± 4.4%, at ages 4–8, respectively, adjusting for height. The 12% of the boys on casein-free diets had an overall % deviation of −18.9 ± 3.7%, nearly twice that of boys on minimally restricted or unrestricted diets (−10.5 ± 1.3%, p < .04), although even for boys on minimally restricted or unrestricted diets the % deviation was highly significant (p < .001). Our data suggest that the bone development of autistic boys should be monitored as part of routine care, especially if they are on casein-free diets.