Childhood obesity is reaching epidemic proportions throughout the world; however, little is known on the nutritional status of children with disabilities. To address this issue, medical records of 748 children aged 18 years or younger receiving physical therapy during 2004-2005 at a privately sponsored free rehabilitation clinic in Punta Arenas, Patagonia, Chile were abstracted. Data included demographic, clinical, and anthropometric information recorded at the first visit. As a comparison, height and weight were also collected in 215 children attending local schools. Nutritional status was calculated as body mass index (above 6 years of age) or evaluated by growth curves (6 years of age or below) as undernourished, normal, overweight, obese, or morbidly obese. Logistic regression was used to determine risk factors for obesity in these children. Overall, a significant difference in nutritional status between disabled and non-disabled children was found (P<0.001). Children with disabilities had a higher prevalence of both below and above normal weight than non-disabled children. Risk factors for obesity included increasing age and living with a grandparent independent of other socioeconomic factors. Compared with normal children, risk of obesity was doubled for those with developmental delays [odds ratio (OR): 1.96; 95% confidence interval (CI): 1.16-3.34] and neurological disorders (OR: 2.58, 95% CI: 1.26-5.29), whereas individuals with cerebral palsy were less than half as likely to be obese than non-disabled children (OR: 0.46, 95% CI: 0.20-1.03). We conclude that overnutrition continues to be a problem for both disabled and non-disabled children in Patagonia. Programs to increase physical activity and improve nutrition are needed in this isolated part of the world.