Objectives To test the hypothesise that the treatment protocol used for preparation of the endometrium for frozen embryo transfer (ET) has a beneficial effect on the disorganised endometrium in women with endometriosis and leads to a higher pregnancy rate. Study design We performed a retrospective, database-searched cohort study. Relevant information was collected from the electronic records of women who underwent IVF/ICSI between 1/1/2000 and 31/12/2008 in our unit. Endometriosis patients formed the study group. The rest of the women formed the control group. The two groups were subdivided, depending on whether they had fresh or frozen ET. The main outcome was live birth rate (LBR). Secondary outcomes were clinical pregnancy rate (CPR) and miscarriage rate (MR). Comparisons were performed by Chi-square and Mann–Whitney tests (SPSS 16.0). Results A total of 3763 fresh and 3523 frozen ET IVF cycles were included in our study, of which 415 (5.7%) were due to endometriosis related subfertility. In the non-endometriosis group, fresh ET had significantly higher LBR, CBR and MR than frozen ET. In women with endometriosis, down-regulated frozen ET cycles had a markedly high LBR and CPR (16.9%, 18.2%), comparable to the LBR and CPR of fresh ET cycles in the same group (19.5%, 20.2%). No significant differences were found in the LBR and CPR in fresh ET cycles between the study and the control group. In frozen ET, however, the CPR was significantly higher in the endometriosis group (18.2% versus 12.7%, P =0.048). Conclusion Unlike the general IVF population, in women with endometriosis undergoing IVF, the preparation of the endometrium for frozen ET with GnRH agonists compared to fresh cycles is associated with higher LBR (16.9% versus 11.9%) and a significantly higher CPR (18.2% versus 12.7%, P =0.048). These results suggest that, in cases of endometriosis, the combined effect of GnRHa on the endometrium and the low level of ovarian steroids may simultaneously offer a better endometrial environment for implantation which may lead to better outcomes.