Background: Polycystic ovary syndrome is the most common endocrine disorder in women, which causes many disorders including diabetes. Objectives: The present study aimed to determine changes in adipose levels and visceral adiposity index after 12 weeks of intense interval training in women with polycystic ovary syndrome in Kermanshah city. Methods: This quasi-experimental study recruited 24 women with polycystic ovary in Kermanshah in 2017. First, 24 women were selected by convenience sampling and then they were divided into two groups of 12 patients. Interval training was performed continuously in the study group 3 sessions per week for 12 weeks. Serum levels of adipose and visceral adiposity index were determined before and after the exercise program through blood sampling and in laboratory conditions. Data was analyzed in SPSS software version 20 using paired t-test and independent t-test. Results: The results revealed no significant difference in adipose levels after 12 weeks of intense interval training in the study group (P < 0.05). But a significant difference was observed in visceral adiposity index before and after the intervention in the study group (P < 0.05). Conclusions:Intense interval training has a favorable effect on the visceral adiposity index in women with polycystic ovary syndrome and can be recommended as a safe treatment for these patients.