Background: Risk for atherosclerotic cardiovascular disease (CVD) and association with abdominal obesity have not been extensively studied in genetic syndromes associated with intellectual disability. Methods: A cross-sectional study was conducted in individuals aged 20-43 years with Williams syndrome (WS; n = 21), Prader-Willi syndrome (PWS; n = 20), and Down syndrome (DS; n = 31). Established metabolic risk factors of CVD were assessed. Results: High prevalence of hypertension and type 2 diabetes was seen in the group with PWS, whereas low prevalence rates were found in the group with DS. In the group with WS, we found a high prevalence of hypertension and a trend towards increased risk of type 2 diabetes, combined with better blood lipid profile. Abdominal obesity was prevalent in all 3 subgroups and was associated with an increased risk of hypertension and metabolic syndrome. Conclusion: PWS and WS had increased risk of CVD. In order to prevent CVD in these groups, regular assessments of the known risk factors are recommended.