The purpose of this study was to compare the effects of an aerobic exercise and Pilates on the different fitness factors and body fat percentage. The subjeacts consisted of 30 inactive women aged 20 to 40 years who was inactive randomly divided aerobics group (age: 28.4±2.99 years, Height: 163.4±5.97 cm, weight: 65.8±6.37 kg), Pilates group (age: 28.8±2.49 years, Height: 162.8±3.46 cm, weight: 65.7±4 kg) and control group (age: 29.7±3.09 years, Height: 162.3±3.77 cm, weight: 64.7±5.38 kg). The aerobics and Pilates exercise protocol with regard to the principle of overload, by the heart rate of the participants was developed. The aerobics and Pilates exercises for six weeks, three days per week for 50 to 60 minutes of exercise performed. The flexibility with sit and reach test, the abdominal muscle endurance with sit-ups test, shoulder girdle muscle endurance with swimming test, aerobic fitness with Racport test and body fat percentage by three points method in pre and post-test were measured. Covariance test and Bonferoni post hoc test using spss software, assuming p≤0.05 was used for data analysis. The results show a significant increase flexibility and shoulder girdle muscle endurance Pilates group was compared to the Aerobic group (respectively: P=0.006, P=0.009 ). Abdominal muscle endurance and aerobic fitness with a significant increase in the aerobic group relative to the Pilates group (respectively: P=0.04, P=0.001) and the fat percentage and body weight was also reduced in the Aerobic group was more significant than that of Pilates group (respectively: P=0.02, P=0.04). However, Pilates and aerobics groups than the control group on all factors, physical fitness, body fat percentage and body weight improved significantly. The results of this study indicate that two exercises for reducing body fat percentage and increasly fitness is switable but aerobic to Pilates is more than adequate.