〔Abstract〕 Objective To investigate the differentially expressed genes(DEGs) and their functions in endometriosis and to screen potential biomarkers and candidate therapeutic drugs. Methods The stromal cells in ectopic endometrium and normal endometrial tissue were sorted by magnetic beads and analyzed for gene expression profile. Combined with the similar chip data on the same platform available in the GEO database, the DEGs were screened using the limma software package and empirical Bayes method, and GO and KEGG enrichment analysis was performed. The STRING database was queried for PPI interaction network analysis to screen the core pathogenic genes. Then, the CMAP database was retrieved to screen the drug-like small molecules. Results There were significant differences in the expression of 869 genes in ectopic endometrium, of which 17 were up-regulated while 852 were down-regulated. GO enrichment analysis showed that the DEGs mainly regulated receptor ligand activity, channel activity and passive transmembrane transporter activity. KEGG enrichment analysis found that DEGs mostly mediated neuroactive ligand-receptor interaction pathway, cytokine-cytokine receptor interaction pathway and IL-17 signaling pathway. PPI network showed that FPR2, SAA1, RLN3, CXCL8, FPR1, PF4, CCR7 and CXCL5 were the core pathogenic genes. The CMAP database showed that thioronine and flunarizine had potential value in the treatment of endometriosis. Conclusion FPR2, SAA1, RLN3, CXCL8, FPR1, PF4, CCR7 and CXCL5 are potential biomarkers for endometriosis. Liothyronine and flunarizine are drug candidates for the treatment of endometriosis.