Introduction: Functional ovarian (FU) cysts represent the most common type of ovarian cysts in women in the reproductive age group. They are mostly asymptomatic and may disappear without treatment within three months. The appropriate management of functional ovarian cysts is the most controversial problems facing gynecologists today despite the different treatment modalities. Aim of the study:The study aimed to assess the efficacy of Doxium versus chymotrypsin on the resolution of simple ovarian cysts.Subjects and Methods: 100 patients with functional ovarian cysts were included in this randomized controlled study without previous ovarian cysts management before. The patients were divided into two equal groups, each with 50 women. Group A included women treated with Doxium, where group B had the women treated with Alphintern. All patients attended the outpatient clinic after the end of menstruation for three consecutive months for a transvaginal ultrasound.Results: Both lines of treatment resulted in the management of FOC, with persistence percentage in doxium and alphintern (20% and 5%, respectively), but doxium has better results in a patient with normal BMI than obese and overweight than alphintern. Conclusion:Doxium and Alphintern proved their effectiveness in FOC management (new novel), but we need to increase the dose of doxium in overweight and obese patients. Moreover, alphintern is more efficient in the improvement of functional ovarian cyst in overweight and obese patient.