The aerobic and anaerobic bacterial flora in the first voided and in the midstream urine of healthy females (n = 5) and female patients with either urethral syndrome (US) (n = 5) or interstitial cystitis (IC) (n = 14) were studied. Bacteria were grown on media enabling isolation of fastidious and aerobic as well as obligatory anaerobic species. In healthy females only gram-positive rods were found whereas US patients also harbored streptococci. Patients with IC presented also with Enterobacteriae and anaerobic bacteria. Five IC patients with severe symptoms were treated with metronidazole; 2 out of 3 patients with anaerobic bacteria in the pretreatment specimens had no anaerobes after metronidazole therapy and in 1 patient streptococci disappeared after the therapy. One patient with severe symptoms and Bacteroides fragilis in the midstream urine became symptom-free after 2 weeks of metronidazole treatment. Although there is uncertainty whether the US and IC are not related to an infectious etiology, the bacterial flora in urethral and in midstream urine in these conditions differs considerably from that of healthy females.