Inflammatory neovascularization is associated with the dynamic formation of select lipid autacoids. Endogenous lipid autacoids were quantified in corneas without injury and after 2, 4, and 7 days of chronic injury by MS based lipidomic analyses using triple quadrupole LC/MS/MS system (MDS SCIEX QTRAP 3200). Specific transition ions and multiple reaction monitoring was used to measure levels of >20 eicosanoids in a single mouse corneas. Significant levels of prostaglandin E2 (PGE2), 15-hydroxyeicosatetraenoic acid (15-HETE), thromboxane B2, 5-hydroxyeicosatetraenoic acid (5-HETE), and 12S- hydroxyeicosatetraenoic acid (12-HETE) were detected in injured and uninjured corneas (n = 4, *P < 0.05 versus uninjured, **P < 0.05 versus 2 D).