Background The World Health Report 2002 of the World Health Organization estimated that physical inactivity is one of the 10 main causes of morbidity and mortality and that the proportion of people whose health is at risk due to a sedentary lifestyle is approximately 60%. Objective To assess the relationship of physical activity level with cardiovascular risk factors and metabolic syndrome in 61 healthy men. Methods The short version of the International Physical Activity Questionnaire (IPAQ) recommended by the World Health Organization was used as a valid measure to estimate two categories of physical activity, low (insufficient and sedentary) and vigorous (moderate and very active). Cardiovascular risk factors and metabolic syndrome were defined using the criteria of the National Cholesterol Education Program of the United States and the International Diabetes Federation respectively. Serum levels of C-reactive protein and ferritin were also measured, and insulin sensitivity was estimated using the Homeostatic Model Assessment-Insulin Resistance (HOMA-IR). Results Mean population age was 47.1 ± 6.9 years. Seventeen participants (28%) had metabolic syndrome. There were no differences between the categories of low and vigorous physical activity, nor a relationship with total physical activity (MET x week). No association was observed between low levels of physical activity and metabolic syndrome criteria. Conclusions The high prevalence of physical inactivity found in study participants using the IPAQ questionnaire was not associated with cardiovascular risk factors and metabolic syndrome.