The identification of biomarkers and their interaction network involved in the processes of endometriosis is a critical step in understanding the underlying mechanisms of the disease. The aim of the present study was to construct biomarker networks of endometriosis that integrated human protein-protein interactions and known disease-causing genes. Endometriosis-associated genes were extracted from Genotator and DisGeNet and biomarker network and pathway analyses were constructed using atBioNet. Of 100 input genes, 96 were strongly mapped to six major modules. The majority of the pathways in the first module were associated with the proliferation of cancer cells, the enriched pathways in module B were associated with the immune system and infectious diseases, module C included pathways related to immune and metastasis, the enriched pathways in module D were associated with inflammatory processes, and the majority of the pathways in module E were related to replication and repair. The present approach identified known and potential biomarkers in endometriosis. The identified biomarker networks are highly enriched in biological pathways associated with endometriosis, which may provide further insight into the molecular mechanisms underlying endometriosis.