Objective Low dose stimulation (LS) is emerging as an alternative regime in assisted reproductive technology (ART). This study aimed to compare the cost-effectiveness of LS to the high dose GnRH antagonist (Atg) regime. Methods An observational prospective study conducted at an academic infertility unit from January to June 2007. Outcome measures included the numbers of follicles, oocytes and embryos, morphological quality of oocytes and embryos, clinical pregnancy (PR) and complication rate. Result Ninety five first attempt ICSI cycles consisting of 54 LS and 41 Atg were analyzed. Subjects in both groups had comparable sociodemographics and reproductive characteristics. LS generated significantly fewer follicles, total oocytes, mature oocytes (all p<0.0005) and immature oocytes ( p=0.009) than Atg but the number of excellent quality oocytes was similar. Significantly fewer embryos were available in LS although the proportion of usable embryos was higher, 83.2% vs. 67.0% for Atg. Mean embryos per transfer was 2.0±1.1 vs. 2.6±1.0 ( p=0.02) for a clinical PR per transfer of 43.2% vs. 50.0% for LS and Atg respectively. LS regime had a shorter gonadotrophin administration period with resultant COH cost one third of the Atg protocol (both, p<0.0005). The cost per live birth per started cycle worked out to be USD 13,200 and 24,900 for LS and Atg respectively. Furthermore, LS had fewer incidences of OHSS compared to the Atg regime, 3.7% vs. 12.2%. Conclusion LS cost benefits included lower amounts of gonadotrophin used and fewer injections. It is a viable alternative regime in producing comparable clinical PR at lower cost and less complication in ART.