Endometriosis is characterized by the presence of endometrial stroma and/or glands outside the uterine cavity, affecting women with severe dysmenorrhea and infertility. Deep bowel endometriosis relates to acute symptoms due to intestinal infiltrative lesions and high density of nerve fibers. The present study analyses the proteome of eutopic endometrium of patients with stage II (EII, n = 8) and stage IV (EIV, n = 6) deep bowel endometriosis as compared to healthy women (HW, n = 7). University ethics committees approved the research. Samples were collected during laparoscopic surgery of EII and EIV patients, and from women having tubal ligation (HW). Digested endometrium proteins were analyzed by mass spectrometry, and resulting files, processed by SEQUEST HT algorithm and Proteome Discoverer 2.5 (Thermo Fisher Scientific, USA). Protein profile comparisons and definition of differentially expressed proteins (DEPs) were based on Peptide Spectrum Matches (PSMs), Linear Discriminant Analysis (LDA), hierarchical clustering (NW vs EII; HW vs EIV and EII vs EIV), and integrated intensity area of the peaks (Progenesis QI; Nonlinear Dynamics, USA). MetaboAnalyst platform was used for multivariate analysis, followed by Tukey's test (RStudio). Bioinformatics tools evaluated protein functional annotations, protein-protein interaction networks, hubs and bottlenecks. There were 1448, 1623 and 1616 proteins identified in eutopic endometria of HW, EII and EIV patients, respectively. Considering 144 DEPs, 19 showed the same trend of expression based on PSMs, LDA, and intensity values. In this group, 18 proteins were upregulated and C3 had lower content in EII and EIV subjects. Represented modules associated with protein profiles protein synthesis and translation, chromatin organization, RNA splicing/processing, cytoskeleton organization, redox homeostasis, metabolism, protein folding and stress response, immune system, vesicle-mediated transport and proteolysis. From healthy to EII and EIV subjects, most modules showed increased expressions. However, apolipoproteins, peptidase/protease inhibitors and immune system components were downregulated in endometriosis patients. Transition from stage II to stage IV was characterized by upregulation of proteins from the SnRNP complex, involved in RNA splicing/processing. Proteins such as SNCA, APOB and B2M were found in HW hubs/bottlenecks, while KRAS, in hub/bottlenecks for EII patients. Progesterone receptor and MAOA resulted in EII-specific bottlenecks, while RELA was among EII-specific hubs and CASP3 was present in EIV-specific hubs/bottlenecks. SEC13 and SEC31A were common in EII and EIV hubs/bottlenecks, characterizing the early stages of the disease. In conclusion, this study highlights the proteome landscape of endometria of patients with deep bowel endometriosis. Proteins characterizing the disease relate to vital functional modules, being potential targets for early diagnosis and development of new therapies.