The association between the intensity of physical activity and the incidence of cardiovascular diseases (CVD), irrespective of energy expenditure (EE), requires further study. Our objective is to examine this relationship using data from a large Spanish cohort. The Seguimiento Universidad de Navarra cohort is formed of university graduates recruited from March 1999 to October 2015. We included 18,737 adults free of CVD (mean age 38 years, 61% women), with a median follow-up of 10.3 years. We estimated the average intensity of leisure time physical activity (LTPA) using a validated questionnaire. We classified respondents into 3 groups: Inactive, <6 average metabolic equivalents (METs) and ≥6 average METs. We used Cox proportional hazards models adjusted by the EE in LTPA (MET-h/week) and other confounding factors, to examine this association. During 1,72,299 person-years of follow-up, we registered 127 cases of CVD (myocardial infarction, stroke, and death due to cardiovascular causes). The adjusted hazard ratio for CVD was 0.76 (95% CI 0.48 to 1.21) in the lower intensity group, and 0.31 (95% CI 0.12 to 0.79) in the higher intensity group, compared with the inactive, with a linear trend (p = 0.03). In conclusion, given the same level of EE, those respondents engaged in higher intensity LTPA, had a lower risk of CVD.