Background: One strategy for managing recurrent uncomplicated urinary tract infections (UTIs) is prevention. This study tested OM-89S, a lyophilized lysate of 18 Escherichia coli strains manufactured using a modified lytic process. Methods: This was a randomized, double-blind trial in 451 female subjects with recurrent uncomplicated UTIs. Period 1 of the study tested 6 mg of OM-89S versus placebo (3 months), plus a 3-month observation. Period 2 of the study was a 3-month treatment period (each monthly cycle consisted of 6 mg of OM-89S daily for 10 days and placebo for 20 days, vs. 50 mg nitrofurantoin daily for 30 days), plus a 3-month observation. Results: There was no difference in the mean rate of UTI episodes between the OM-89S (0.66 ± 0.93) and placebo groups (0.63 ± 0.86; p = 0.95) in period 1. Similar findings were obtained for period 2. OM-89S was well-tolerated. Conclusions: Our results did not demonstrate a preventive effect of OM-89S compared to placebo. This may be due to the low number of UTIs that occurred during the study, the high number of protocol violations, and/or the modified manufacturing process used for OM-89S.