BACKGROUND. Propionibacterium sp. and Staphylococcus spp. are the most frequent bacteria cultured from prostatectomy specimens but are seldom detected by universal eubacterial PCR. MATERIALS AND METHODS. We obtained from GenBank representative 16S rRNA gene sequences from Propionibacterium sp., Staphylococcus spp. and from 34 bacterial genera that were recently detected in prostate tissues using universal eubacterial PCR. We compared these 16S rDNA sequences with the universal eubacterial 16S PCR primer sets chosen for detection of bacterial DNA in prostate tissues. RESULTS. We show that failure to detect DNA from Propionibacterium sp. and Staphylococcus spp. in prostate tissues is strongly associated with the presence of mismatches near the 3 ' termini of the 16S rDNA primer sets used. CONCLUSIONS. The choice of 16S PCR primers may play an important role in determining the spectrum of bacterial genera detected in prostate tissue by universal eubacterial PCR.