The objective of this study was to determine the rates of apoptotic cell death in ovary and thymus collected from wild female cotton rats (Sigmodon hispidus) inhabiting five petrochemical-contaminated and five ecologically matched reference sites in Oklahoma. Overall comparison of reference and contaminated sites, using individual sites as replicates, revealed a significantly increased rate of ovarian cell apoptosis in cotton rats inhabiting contaminated sites. In comparison to rats from reference sites, the number of uterine scars was lower in rats collected from the contaminated sites. There were no significant differences in the percentage of atretic follicles among animals collected from reference and contaminated sites. The rate of thymocyte apoptosis was elevated at one of five contaminated sites, although the overall rate of thymocyte apoptosis was not significantly different when comparing all sites. To our knowledge, this is the first study documenting elevated rates of ovarian and thymic cell apoptosis in wild mammals exposed chronically to environmental toxicants.