Abstract: Here, we determined basic differentially expressed genes in endometrial lesions compared to eutopic endometrium of the patients with endometriosis (EM). Endometrial biopsy and tissue sampling were performed in ten women with pelvic EM and nine controls at their mid-secretory phase. NGS of mRNA combined with bioinformatic analysis and complemented by RT-qPCR analysis were used for analysis. A list of differentially expressed genes of ectopic compared to eutopic endometrium during mid-secretary phase has been composed. Functional annotation has found profound gene expression perturbations in numerous EM pathways including extracellular matrix, complement and coagulation, as well as cell cycle-related gene family. The genes of alcohol dehydrogenase 1B (ADH1B) and fatty binding protein 4 (FABP4) were determined as the most dramatically up-regulated genes in ectopic endometrial lesions. Both genes were not reported before to be associated with EM. Several other genes including PLA2G2A were also up-regulated in ectopic EM lesions. Notably, FABP4 and ADH1B are key genes in basic metabolism and known for their function in adipose tissue. The results provide intriguing new avenue for endometriosis studies.