The effectiveness of two aerobic exercise programs on the modification of the metabolic syndrome (MS) components and its influence in reducing cardiovascular risk was evaluated in 16 sedentary women (30-66 years old). Patients were randomly divided into two exercise groups: continuous training (CE: 45 minutes at 65-70% of heart rate reserve or HRR) or interval training (IE: 5 x 3 minute intervals at 80-85% HRR with two minutes of active recovery at 65-70% HRR), and each participant gave previous informed consent. The components of MS were assessed according to the criteria for women of the National Cholesterol Education/Third Treatment Adult Panel, and cardiovascular risk factors at baseline and 16 weeks later. Data analyses were performed with the Wilcoxon signed test and the Mann-Whitney U-test (SPSS v. 12.0 Windows: p < 0.05). Both exercise programs were effective in the modification of a number of MS components (triglycerides, systolic/diastolic blood pressure), however IE had a higher percentage of patients without MS diagnosis at the end of the study (62.5%). The CE improved the physical fitness by increasing the VO₂peak and METs and decreasing heart rate recovery, which is reflected on the reduction of cardiovascular risk.