Abdominal obesity (AO), measured by waist circumference (WC), is a stronger predictor of subsequent development of cardiovascular disease (CVD) than generalised obesity, which is measured by body mass index (BMI). This study aimed to measure WC and prevalence of AO in Malaysians visiting primary care physicians. 1893 patients between the ages of 18 and 80 attending primary care clinics in Malaysia were recruited over two days for this multi-centre cross-sectional study. Pregnant women were excluded, their medical history, weight, height and WC were examined. The prevalence of co-morbidities were as follows: (1) CVD-4%, lipid disorder-17%, hypertension-26%, diabetes-14% and any of the clinical characteristics of CVD/lipid disorder/hypertension/diabetes-38%. The mean BMI for men and women was 25.62 +/- 4.73 kg/m2 and 26.63 +/- 5.72 kg/m2, respectively. Based on WHO criteria for BMI (overweight, 25-29.9 kg/m2; obese, > 30 kg/m2), 34.2% were overweight and 20.4% were obese. The mean WC for men and women was 89.03 +/- 13.45 cm and 84.26 +/- 12.78 cm, respectively. Overall, 55.6% had AO and there was higher prevalence among women (based on International Diabetes Federation criteria: WC > or = 90 cm for men and > or = 80 cm for women). AO was present in approximately 71% patients with lipid disorder, in 76% with hypertension and in 75% with diabetes. Patients with AO were also at a higher risk of developing co-morbidities. Malaysia has a high prevalence of AO and associated cardiovascular risk factors. This needs to be addressed by public health programs, which should also include routine measurement of WC.