The objective of this prospective randomised controlled study was to compare the cost-effectiveness of a low cost antagonist protocol using oral ovulation inducing agents (Clomiphine Citrate or Aromatase Inhibitors) with a standard long GnRH agonist protocol in IVF-ICSI cycles. IVF-ICSI cycles at our centre from 2006 to 2012 were prospectivly studied for gonadotropin usage and cost effectiveness. The patients in the study underwent a long GnRH-Agonist or an Antagonist protocol after randomisation using a computer generated list. The antagonist protocol patients were given only oral ovulogens (Clomiphine Citrate or Aromatase Inhibitors) for the first five days of cycle, followed by gonadotropins. A total of 346 IVF-ICSI cycles were prospectivly studied in patients less than 40 years of age. All patients received low-dose oral contraceptive pills in the preceding cycle. They were randomised into two groups using a computer generated list. The agonist group underwent the standard long GnRH analogue protocol. The antagonist group received oral ovulation inducing agents (Clomiphene Citrate / Aromatase Inhibitor) for the first five days of cycle followed by gonadotropins and 0.25mg antagonist (Cetrorelix) injection daily till the day of hCG, using a flexible antagonist start approach. There was a significant difference in the gonadotropin usage between the two groups. As a result, the cost of the oral ovulation inducing agents (Clomiphene Citrate / Aromatase Inhibitor) - gonadotropin - antagonist cycle was significantly lower than the long GnRH agonist - gonadotropin protocol. Though the mean number of oocytes retrieved was higher in the long protocol group, yet the clinical pregnancy rate per transfer was similar in both the groups. Use of GnRH antagonist in combination with oral ovulation inducing agents offers the advantage of an economical method of stimulation in IVF-ICSI cycles, as compared to the agonist protocol, with a similar pregnancy rate.