The impact of environmental pollutants on gynecological disorders is mediated by inflammation and oxidative stress, but little is known about the interaction of oxylipins, bioactive lipids derived from polyunsaturated fatty acids that play an important upstream role in regulating of these biological processes. The aim of this study was to explore factors influencing the levels of oxylipins and their precursor fatty acids in the serum of women undergoing in vitro fertilization (IVF), including internal exposure to chemical pollutants and underlying gynecological disorders in infertile women. We analyzed the serum of 100 women recruited at the Nantes University Hospital with female infertility related endometriosis, polycystic ovaries, ovarian insufficiency or unexplained. Fertile women consulting for male infertility or being oocyte donors were also included as a control group. The concentrations of ten oxylipins were determined in serum using negative electrospray liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), after protein precipitation and SPE-based extraction. Twenty-six free fatty acids were subjected to liquid-liquid extraction and derivatization before detection by gas chromatography coupled to a flame ionization detector and mass spectrometry system (GC-FID/MS). Negative associations were found between the fluorinated industrial pollutant, perfluoroundecanoic acid (PFUnA) and levels of prostaglandin E2, 15-hydroxyeicosatetraenoic acid (15HETE) and 5-HETE. Levels of 5-HETE and 8,9-epoxyeicosatrienoic acid were found to be at lower levels in women with endometriosis-related infertility. Further research will be conducted to better understand the potential role of oxylipins on the functional associations between environmental pollutants and gynecological disorders.