Oxidative stress is thought to be an important pathogenic mechanism in many diseases of the retina. The purpose of this study was to investigate the chemical changes that are present in the photoreceptor outer segments of the retina following exposure to oxidative stress. Fourier transform infrared (FT-IR) microspectroscopy enables the characterization and semi-quantitation of chemical functional groups in microscopic regions of tissue sections. This technique was used to evaluate the chemical changes in the outer segments following exposure to ferrous sulfate, which promotes oxidative tissue damage. A reduction of C=C-H and C=O functional groups was observed in the outer segments of iron-injected eyes compared to vehicle-injected eyes at 3 days following injection, which is prior to major histological changes that occur by 7 days. These functional groups are found in docosahexaenoic acid (DHA), which is present at a high concentration in the outer segments. DHA contains a series of six cis-conjugated double bonds, which are vulnerable to free radical attack, and the reduction of these unsaturation group absorptions suggests that DHA was degraded and/or removed from the outer segments. An unexpected finding was that several other chemical functional groups increased in concentration over time in the outer segments of vehicle-injected eyes compared to non-injected eyes. These increases generally did not include C=C-H or C=O, which suggests that either DHA was being degraded while other organic molecules were being concentrated, or that production of DHA failed to be upregulated in vehicle-injected eyes. In summary, there was a loss of both C=C-H and C=O functional group concentrations in the outer segments of iron-injected eyes, and there was an increased concentration of several other chemical functional groups following trauma induced by vehicle injection.