The impact of ER XbaI and PvuII α gene polymorphisms on overweight and obesity were studied in 77 subjects with Down Syndrome (DS), of which 32 were children (18 boys, 14 girls), mean age 8.7 ± 2.3 years, and 45 adolescents (28 boys, 17 girls) mean age 14 ± 2.5 years. Their lifestyle was compared to 40 healthy age-matched controls. DS subjects had significant lesser physical activity than controls (p<0.05) and a lower caloric intake than the recommended requirements, which was significantly lesser than controls (p<0.05). Body Mass Index (BMI), Arm Circumference (AC) and Triceps Skinfold Thickness (TST) were significantly higher in DS subjects than controls (p<0.05), while metabolic and cardiovascular parameters were not significantly different between the groups (p>0.05). The frequency of ER genotypes in DS subjects was compared with the healthy controls, finding that there was a high prevalence of XXER genotype in DS subjects. Children and adolescents with DS, lacking ER XbaI site, showed significantly higher BMI and body fat distribution than other XbaI genotypes. The lack of ER XbaI site can indicate added risk of obesity in DS. No differences in metabolic and cardiovascular parameters were observed among ER genotypes. However, childhood obesity is associated with increased cardiovascular risk.