A noninvasive diagnostic test for endometriosis is needed to shorten the current diagnostic delay of 8-11 years. The goal of this study was to discover new biomarkers for endometriosis using an antibody array approach. A total of 103 plasma samples from patients with laparoscopically confirmed presence (n = 68) or absence (n = 35) of endometriosis were selected. Samples were pooled according to disease status, cycle phase, disease stage, and phenotype. Pooled samples were screened for possible biomarkers using the L-series 1000 and Quantibody 660 arrays from RayBiotech. Technical verification of ten markers was done using a custom-made multiplex immunoassay identifying ten proteins (10-plex) and later by single ELISA. Due to the limited reproducibility of the L-series 1000 immunoassay, the biomarker screening was performed using the Quantibody 660, a sandwich-based multiplex immunoassay, which showed that 280 proteins were upregulated, and 29 proteins downregulated in the endometriosis pool versus the control pool. In order to assess the reproducibility of these results, ten preselected proteins were analyzed using a custom 10-plex. Four proteins (CD48, DNAM-1, IL-31, and XIAP) were confirmed to be differentially expressed when comparing the endometriosis and control pool. However, only IL-31 showed a univariate statistical difference between endometriosis and control groups in individual samples that were part of the initial pools. In conclusion, discovery and verification of potential markers proved challenging using multiplex immunoassay methods, mainly due to issues with reproducibility. Only IL-31 showed potential as possible biomarker for endometriosis.