Objective: Increasing use of Assisted Reproductive Technologies (ART) ,make the investigation on its complications more necessary. One of the main concerns in this regard is the side effects of medications required for controlled ovarian stimulation. Systemic and local reactions to the medications, Ovarian Hyper Stimulation Syndrome (OHSS) and genetic changes which can lead to cancer must be checked in treatment of infertile patients. In this study, cytogenetic effect of Buserelin, which is a gonadotropin hormone agonist (GnRH agonist), has been evaluated during In-Vitro Fertilization (IVF) cycle. Materials and Methods: Blood samples were taken from 40 females refer to Royan institute(25 females in ART cycle use Buserelin from day 15 to day 2 of second menstrual cycle and 15 normal fertile women as control), cultured and examined by Sister Chromatid Exchange (SCE) assay, considered as the most sensitive mammalian system for measuring the effects of mutagenic carcinogens. Also the changes of 17β-stradiol (E2), which is known to produce adverse effects such as embroyotoxicity, teratogenicity and carcinogenicity by DNA damaging, were evaluated in days 15 and 2 of menstrual cycles of both patients and control group. Results: In both groups, evaluation of SCE frequencies demonstrates lower rate around early follicular phase as compared to ovulation time, because of lower dosage of E2. More decreased SCE frequency was observed after Buserelin injection because of its inhibited effect on E2, which result to grater decrease in E2 dosage. Conclusion: Finally, results indicated that Buserelin doesn’t seem to have a significant potential for induction of malignancies after ovulation induction treatment and other medications in ovulation stimulation must be checked.