The purpose of the present research was to determine the effects of intermittent and continuous training programs on some selected cardiovascular risk factors in young obese females. For this purpose, 36 obese sedentary subjects with BMI>30 were randomly assigned to three groups of intermittent exercise (mean ± SD of height, weight, and age: 163.2±5.8cm, 86.8±11.8kg, 20.7±1.3yr), continuous exercise (160.2±6.4cm, 83.8±9.5kg, 22.1±2.2yr) and control (166.2±7.1cm, 86.6±10.5kg, 22±2.4yr). The intermittent group participated in eight weeks (three sessions per week) of 800 meters (4× 200m) exercise with 80%-90% of reserved heart rate and 1/3 rest interval whereas the continuous group ran this distance with 60%-70% of reserved heart rate with no rest interval. A distance of 400 meters (2×200 meters) was added to the primary distance every week in the intermittent group and 400 meters in the continuous group. Before and after the protocol, HDL, LDL, CHOL and VLDL were measured by Alpha-X auto analyzer apparatus. Also, weight and height of the subjects were measured at the beginning and the end of the protocol. The control group only participated in pretest and posttest. To analyze the data, one-way analysis of variance, paired t-test and LSD post hoc test were used. The results showed that TC significantly decreased in the intermittent group whereas HDL significantly increased. HDL significantly increased (p=0.03) while LDL (P=0.004), TC (p=0.05), VLDL (p=0.05) and the weight of the participants (p=0.005) decreased significantly in the continuous group (P>0.05). The results also showed a significant change in weight (p=0.005), TC (p=0.001), HDL (p=0.009) and VLDL (p=0.004) in the posttest for all three groups (P>0.05). These significant differences existed between control group with intermittent and continuous groups while there was no significant difference between intermittence and continuous groups. There was no significant change in TC and LDL in the posttest of all groups. It was concluded that both types of exercise positively changed cardiovascular risk factors in obese female subjects.