Background: The techniques used in assisted reproductive technologies have progressed considerably, but many embryos do not implant after transfer upon the use of these techniques. One of the causes of infertility is repeated implantation failure due to decreased endometrial receptivity. Furthermore, in clinical conditions such as endometriosis and myoma, implantation decreases after embryo transfer. In this case-control study the expression patterns of HOXA-10 and BTEB1 mRNAs were evaluated at the time of implantation in patients with myoma and endometriosis.Methods : In this study performed in Hamadan University of Medical Sciences during 1389, the cases included 16 patients with endometriosis and myoma (8 in each group) and the control group consisted of 8 fertile women. Endometrial sampling was performed at mid-secretory phase. Later, the expression patterns of HOXA-10 and BTEB1 mRNAs were evaluated using a semi-quantitative RT-PCR method. Results : The optimal PCR cycles determined were 30, 32 and 26 for HOXA10, BTEB1 and β-actin, respectively. Endometrial HOXA-10 and BTEB1 mRNA expression levels (normalized to -actin expression) at the time of implantation were significantly decreased in the endometrium of infertile patients with endometriosis compared with that of healthy fertile controls (P<0.05). A similar pattern was seen in patients with myomas for both HOXA10 and BTEB1 genes, (P<0.05). Conclusion: It seems that lower expression of HOXA-10 and BTEB1 mRNAs in the implantation window of endometrium that increase normally, could account for some aspects of infertility in patients with endometriosis and myoma.