Background: The aims of this study were to assess the prevalence of obesity in school children with intellectual disabilities and to determine the most appropriate indicators of obesity measurement. Materials and Methods: The weight, height, body mass index (BMI), waist circumference, waist-to-height ratio and body fat percentage as measured by bio-impedance were evaluated in 192 children with intellectual disabilities. Results: According to the BMI, 26% of the children were overweight or obese. An excess of body fat was measured in 44.9% of the boys and 47% of the girls. Excess visceral adipose tissue (a high waist-to-height ratio) was identified in 26.4% of the boys and 36.5% of the girls. Conclusions: The results indicate the high prevalence of obesity in these children and the heightened risk of developing comorbidities due to visceral adipose tissue. Professional staff should be warned of these potential health problems: early identification and management of excess body fat is the best strategy for preventing obesity and comorbidities in adulthood.