Background: The objective of this study was to analyze the incidence and the underlying mechanisms of empty follicle syndrome (EFS) occurring in gonadotropin releasing hormone agonist (GnRHa) triggered in in vitro fertilization (IVF) cycles with GnRH antagonist protocol in women with polycystic ovary syndrome (PCOS) of Indian origin. The study also intended to evaluate the cycle outcome following a rescue trigger. Methods: Retrospective cohort analysis of data was extracted from the hospital database of 271 PCOS patients who underwent IVF in antagonist protocol triggered with GnRHa from August 2014 to December 2016. All cases with failure to obtain oocytes following retrieval were analyzed. Continuous variables were expressed as mean±SD using t-test and Chi-squared test for categorical variables. A p<0.05 was considered statistically significant. Results: Incidence of EFS following GnRHa trigger was found to be 3.3%. False empty follicle syndrome (FEFS) accounted for majority of the cases (8/9=88.8%). Of the nine EFS, six cases were salvaged with a rescue trigger, resulted in transfer of reasonably good quality embryos in a frozen-thawed embryo replacement cycle achieving clinical pregnancy in three cases (3/6=50%). Conclusion: Our experience with EFS cases following GnRHa, albeit small, given the rarity of its occurrence, suggests that majority of EFS are of false forms and can be effectively salvaged which results in reasonably favorable outcome.