Abstract Background Recent data indicate increasing rates of adult obesity and mortality from cardiovascular disease (CVD) in Greece. No data, however, are available on prevalence of overweight and obesity in relation to CVD risk factors among young adults in Greece. Methods A total of 989 third-year medical students (527 men, 462 women), aged 22 ± 2 years, were recruited from the University of Crete during the period 1989–2001. Anthropometric measures and blood chemistries were obtained. The relationships between obesity indices (body mass index [BMI], waist circumference [WC], waist-to-hip ratio [WHpR], waist-to-height ratio [WHtR]) and CVD risk factor variables (blood pressure, glucose, serum lipoproteins) were investigated. Results Approximately 40% of men and 23% of women had BMI ≥ 25.0 kg/m2. Central obesity was found in 33.4% (average percentage corresponding to WC ≥ 90 cm, WHpR ≥ 0.9 and WHtR ≥ 50.0) of male and 21.7% (using WC ≥ 80 cm, WHpR ≥ 0.8, WHtR ≥ 50.0) of female students. Subjects above the obesity indices cut-offs had significantly higher values of CVD risk factor variables. BMI was the strongest predictor of hypertension. WHtR in men and WC in women were the most important indicators of dyslipidaemia. Conclusion A substantial proportion of Greek medical students were overweight or obese, obesity status being related to the presence of hypertension and dyslipidaemia. Simple anthropometric indices can be used to identify these CVD risk factors. Our results underscore the need to implement health promotion programmes and perform large-scale epidemiological studies within the general Greek young adult population.