This study aims to evaluate differences in the expression of proteins present in the peritoneal fluid (PF) of women with and without endometriosis. PF samples were subjected to two-dimensional gel electrophoresis; protein spots of interest were identified by liquid chromatography tandem mass spectrometry. Several molecules had aberrant expression in PF of women with endometriosis; they may be useful for a better understanding of the pathogenesis of this disease.