Guidelines for establishing clinical safety of microbicides in early clinical studies have evolved significantly since the first trials. In addition, because of the difficulty of establishing efficacy of a microbicide prior to Phase III testing, there has been an increasing emphasis on establishing pharmacokinetic (PK)/pharmacodynamic (PD) relationships using genital samples collected in vivo in Phase I studies. A healthy pipeline is critical to success; however, it is unlikely that the majority of microbicide candidates will progress to clinical testing. Those that do enter clinical testing may have different mechanisms of action than early candidates. Given this, drug-specific modifications for early clinical assessment will need to be considered. These emerging issues associated with early clinical trials of microbicides will be reviewed, along with recommendations for future clinical safety and PK/PD evaluation.