Perfluorooctanesulfonate (PFOS) is one of a class of industrial chemicals known as perfluoroalkyl acids, which have a wide variety of uses as surfactants and stain repellants. The presence of fluorochemical residues in human blood, plasma, or serum from sample populations worldwide is indicative of widespread human exposure. Previous studies demonstrated that PFOS alters fatty acid metabolism in the liver of rodents and that this leads to peroxisome proliferation. This study was undertaken to (1) confirm the effects of PFOS on rat liver, (2) identify additional target organs and systems, and (3) further explore the biochemical and molecular changes associated with PFOS exposure. The results confirmed that liver was a primary target for PFOS. Hepatomegaly, decreased serum triglycerides and cholesterol, and increased expression of the genes for acyl-coenzymeA oxidase 1 (ACOX1) and cytochrome P-450 4A22 (CYP4A22) were indicative of exposure to a peroxisome proliferator. Changes in liver fatty acid profiles included increased total monounsaturated fatty acid levels and decreased total polyunsaturated fatty acids, as well as an increase in linoleic acid levels and a decrease in longer chain fatty acids. These changes were similar to those induced by relatively weak peroxisome proliferators. Disruptions in hepatic fatty acid metabolism may contribute to changes in red blood cell membranes, resulting in increased lysis and cell fragility. Serum thyroid hormone levels were decreased in PFOS-treated rats, while the kidney and cardiovascular systems were not significant targets. Residue analyses indicated that PFOS accumulation in tissues was dose dependent, appearing preferentially in the liver at lower doses but increasing in serum and other organs relative to liver at higher doses.