The composition of sulfated glycosaminoglycans (GAGs) and the tissue distribution of chondroitin sulfate (CS) were analyzed in deeply infiltrating endometriosis (DIE) of rectosigmoid, using metachromatic staining, and biochemical analysis employing electrophoresis before and after specific enzymatic or chemical degradations, and immunostaining with an antibody against CS. The sulfated GAGs were characterized as dermatan sulfate (DS), heparan sulfate (HS) and CS; and DS strongly predominated compared to HS and CS. Immunostaining procedures showed that CS was concentrated in the endometriosis foci, distributed throughout the stroma around the glands. This is the first report describing the composition of sulfated GAGs and the tissue location of CS in DIE by means of histochemical, biochemical and immunohistochemical analyses. These results confirmed that in DIE of rectosigmoid, as in eutopic endometrium [Nasciutti, L.E., Ferrari, R., Berardo, P.T., Souza, M.L.S., Takiya, C.M., Borojevic, R., Abrao, M.S., Silva, L.C.F., 2006. Distribution of chondroitin sulfate in human endometrium. Micron 37, 544-550], CS was the dominant sulfated GAG in stroma of the lesion foci.