Contraceptive microbicides formulated as vaginal gels offer the possibility of women-controlled contraception and prevention of HIV infection. However, the effects of these gels on the upper reproductive tract is largely unknown. The purpose of this study was to determine the effects of nonoxynol-9 (N-9) on human endometrium. Human endometrial biopsies were cultured and incubated with various dosages of N-9 for 6 or 24 h. Endometrial histology was assessed by light microscopy using hematoxylin and eosin. Inflammatory response was determined by analyzing proinflammatory cytokines with enzyme-linked immunosorbent assay. Endometrial mucin was assessed by immunohistochemistry and real-time polymerase chain reaction. Histological changes consistent with focal coagulative necrosis were seen after 6 and 24 h of culture. All cytokines (interleukin 1beta, tumor necrosis factor alpha and interleukin 8) decreased at all concentrations of N-9 after 24 h of incubation. The expression of Mucin1 (MUC-1) was inhibited in a dose-dependent manner at both the protein and messenger RNA levels. These results demonstrate for the first time that N-9 has multiple, potential deleterious effects on the human endometrium characterized by necrosis, alteration of proinflammatory cytokines and inhibition of MUC-1 expression. Taken together, these in vitro findings suggest that N-9 can interrupt the functional barrier provided by the endometrium and, thus, facilitate infection with HIV and other pathogens.