The significance and diagnostic value of semen analysis in chronic bacterial prostatitis has been extensively debated and remains controversial. To investigate the diagnostic relevance of semen culture in the bacteriological workup of prostatitis patients, we retrospectively analyzed a clinical database of 696 symptomatic patients. All patients were routinely subjected to a four-glass test, followed by semen culture and analysis. This allowed to dissect from the database three different diagnostic scenarios, and to compare the 'two-glass' pre-/post- massage test and the standard 'four-glass' test with a 'five-glass' test (four-glass plus post-VB3 semen culture). The 'five-glass' test showed 3.6- or 6.5-fold increases in relative sensitivity and lesser reductions (-13.2% or -14.7%) in relative specificity for traditional uropathogens (TUs) compared with the four-glass or two-glass test, respectively. The area under the ROC curve and Jouden's index were increased, whereas positive and negative likelihood ratios were lower than comparators, indicating that the 'five-glass' assay may be superior in confirming the negative outcome of both standard tests. The five-, four-, and two-glass tests detected TUs (Enterobacteriaceae, Enterococci, etc.) in 120, 33, and 20 patients and unusual pathogens (Streptococci, other Gram-positive species, Mycoplasmata, and others) in 130, 56, and 45 patients, respectively. When patients were subjected to pharmacological treatment, including a combination of a fluoroquinolone and a macrolide, no differences in eradication rates were observed between groups diagnosed with different tests, irrespective of pathogen category. Eradication was associated with long-term sign/symptom remission; no significant intergroup differences in sign/symptom scores were observed throughout a 24-month off-therapy follow-up period. In conclusion, our data support the usefulness of semen analysis in the diagnostic workup of prostatitis patients when this test is used to complement the four-glass Meares and Stamey test. Improvement of microbiological assays conveys important diagnostic and therapeutic implications.