Microbicides may interfere with detection of Chlamydia trachomatis (Ct) and Neisseria gonorrhoeae (Ng) in urine samples from women who use microbicides. The inhibitory effects of BufferGel, PRO2000 and PRO2000 placebo, in urine samples, were determined by nucleic acid amplification tests (NAATs). Uninfected urine was inoculated with different concentrations (10(5)-10(1) organisms/mL); microbicides were added to achieve final concentrations from 5% to 0.1%. Specimens were tested using strand displacement amplification (SDA) for Ct and Ng. Samples with BufferGel demonstrated no inhibition. Samples with PRO2000 showed inhibition at the 5% concentration when tested for Ct, whereas for Ng, PRO2000 showed inhibition at 5%, 2% and some 1% concentrations. The placebo showed no inhibition when detecting Ct, and variable inhibition at the 5% and 2% concentrations for Ng. The potential inhibitory effects of microbicides on the NAATs selected for detection of Ct and Ng should be considered in clinical trials involving topical microbicides.