To evaluate the effect of basal ovarian cysts and also the impact of aspiration of those cysts at the onset of an assisted reproductive treatment (ART) cycle on stimulation characteristics and treatment outcome. A retrospective study of 162 normoresponder patients with basal cysts from whom at least five oocytes were retrieved was performed. They all received mid-luteal GnRH-a long protocol. Of 162 patients, 79 with basal cysts of 29.4 ± 9.0 mm and initial estradiol (E2) of 221.2 ± 24.3 pg/ml underwent cyst aspiration on day 3 and stimulation was initiated when E2 fell to <70 pg/ml. In the remaining 83 patients with basal cysts of 16.9 ± 6.4 mm and initial E2 of 39.9 ± 5.7 pg/ml, the stimulation was started with gonadotropins immediately. The cycle characteristics and the treatment outcomes were compared between those two groups. Further comparison was made between the two groups when initial E2 concentrations were <70 pg/ml. No significant differences were found between the two compared groups regarding stimulation parameters and treatment outcomes. Implantation rates (IR) were 27 and 23%, pregnancy rates (PR) were 64 and 54% and live birth rates were 47 and 41% in the cyst positive and cyst aspirated groups, respectively (P > 0.05). Basal ovarian cysts should not be considered a contraindication to gonadotropin initiation in normoresponder ART patients, provided serum E2 levels indicate down-regulation. Moreover, aspiration of basal cysts does not improve ART outcome when E2 levels are suppressed.