Background Metabolic syndrome (MetS) is an important risk factor of cardiovascular disease (CVD) and type 2 diabetes. Previous studies have suggested an inverse relationship between physical activity and MetS. However, these findings were inconsistent, and few investigators have examined these associations among South Americans. We estimated the prevalence of MetS and its association with leisure time physical activity (LTPA) among Peruvian adults. Materials and methods This cross-sectional study of 1675 individuals (619 men and 1056 women) was conducted among residents in Lima and Callao, Peru. Information about LTPA, socio-demographical and other lifestyle characteristics was collected by interview. The presence of MetS was defined using the Adult Treatment Panel III criteria. Results Overall, the prevalence of MetS was 26·9% and was more common among women (29·9%) than men (21·6%). Habitual participation in LTPA was associated with a 23% reduced risk of MetS (OR = 0·77; 95% CI: 0·60-1·03). There was an inverse trend of MetS risk with amount of LTPA (P = 0·016). Compared with non-exercisers, those who exercised <150 min/week had a 21% reduced risk of MetS (AOR = 0·79; 95% CI 0·60-1·04). Individuals who exercised ≥150 min/week, compared with non-exercisers, had a 42% reduced risk of MetS (AOR = 0·58; 95% CI: 0·36-0·93). Associations of similar magnitudes were observed when men and women were studied separately. Conclusion These data document a high prevalence of MetS and suggest an association with LTPA among urban dwelling Peruvians. Further prospective studies are needed to confirm these observations and to examine interventions that may promote increased physical activity in this population. © 2009 Stichting European Society for Clinical Investigation Journal Foundation.