Despite a significant worldwide need for effective microbicides to reduce sexually transmitted diseases (STD) and HIV transmission, none is currently available. C31G, a surface active anti-infective agent that is active in vitro against bacterial and viral STD pathogens, was evaluated in a 3-day, once-daily dosing clinical trial designed to assess multiple formulations for safety and acceptance. The trial used a scoring algorithm that was based on relevant subject reported symptoms and signs observed at follow-up. Differences in tolerance and acceptability between the formulations were demonstrated, as was consistency with the results from a previous 7-day trial that involved two of the formulations (1.2% HEC gel, 2.0% N-9). The 1.0% C31G co-polymer gel was the best tolerated, most acceptable formulation, and will be advanced to longer, more comprehensive trials. Thus, formulation differences are relevant to microbicide tolerance and acceptability, and the 3-day trial design validated in this study can be used to assess formulations.