Topical microbicides, designed for vaginal or rectal administration, are needed to prevent human immunodeficiency virus (HIV) and other sexually transmitted infections (STI). Presently marketed topical microbicides are cytotoxic and damage the vaginal epithelium with frequent use. Rational development of new candidate compounds should build on knowledge of the pathways of microbial invasion. The establishment of assays and models that predict efficacy and safety is critical. Comprehensive pre-clinical evaluation of promising microbicides should include rigorous assessment of the effects of repeated application of topical agents on mucosal inflammatory cells, cytokines, and the genital tract virus population. These studies will lay the groundwork for future clinical trials.