The proteomic content of the endometrial fluid (EF) from patients with endometriosis has been investigated, but the lipidomic profile has not been analyzed yet in detail.This study is a comparative untargeted lipidomic analysis of human EF obtained from 35 patients (12 endometriosis and 23 controls). Global differential lipidomic profile was analyzed in both groups by ultrahigh performance liquid chromatography coupled to mass spectrometry. A total of 123 out of the 457 metabolites identified in the EF were found to be significantly differentially expressed between ovarian endometriosis (OE) versus controls. Univariate statistical analysis showed reduced levels of saturated diacylglycerols and saturated triacylglycerols in endometriosis patients. A predictive model was generated using the 123 differentially expressed metabolites. Using this model, we were able to correctly classify 86% of the samples. This study identified the lipidomic profile in the EF associated with OE, suggesting that EF analysis could be considered as a minimally invasive approach for the diagnosis of endometriosis. In conclusion, the lipidomic profile of the EF is different between samples from patients with OE and controls. © The Authors 2017. Published by Oxford University Press on behalf of Society for the Study of Reproduction. All rights reserved. For permissions, please journals.permissions@oup.com.