We performed a comparative analysis of microbiological and clinical responses to combination therapy in 104 symptomatic patients showing evidence of infection by traditional uropathogens (TU) or by unusual pathogens (UP) at the prostatic level. Eighty-two pathogens out of a total of 104 isolated microorganisms were eradicated at the end of a 6-week course of combination therapy with ciprofloxacin, azithromycin, alfuzosin and a S. repens extract. The TU and UP groups showed eradication rates of 75.5% and 82.3%, and clinical success rates of 78.8% and 85.7%, respectively. Thus, a similar response to therapy was observed in patients infected by TU or by UP. Intergroup differences were not significantly different, with the exception of higher scores relative to the impact of the disease on quality of life in TU-patients. Long-term improvement of signs and symptoms of prostatitis indicates that combination therapy is beneficial for symptomatic patients showing evidence of infection by unusual pathogens at the prostatic level. Our data support the hypothesis that organisms other than the traditionally recognized uropathogens may play a role in the onset of prostatitis.