To identify potential novel biomarkers that differ between subjects with and without endometriosis and that might aid in developing a noninvasive, serum-based diagnostic test. Case-control evaluation of a diagnostic test. University medical center. Consenting women of reproductive age undergoing laparoscopy for indications of pain, infertility, elective tubal ligation, tubal reanastomosis, or other benign indication. Diagnostic laparoscopy and peripheral venipuncture. Concentrations of low-molecular-weight proteins in serum; surgical staging of endometriosis. Six proteins were found that were differentially expressed between those with and without disease and that had good diagnostic properties. Taken together in a two-step diagnostic algorithm, we were able to diagnose 55% of subjects, with 99% accuracy as to the status of disease. Further combining this algorithm with that derived by our previous study of serum putative markers (monocyte chemoattractant protein-1, migration inhibitory factor, leptin, and CA-125) improved our diagnostic capability to 73% of subjects, with 94% overall accuracy. This study is the critical first step in the identification of potential novel biomarkers of endometriosis. Future identification of the proteins and further validation in a second population is needed before applying these findings in clinical practice.