To assess the efficacy and safety of the percutaneous suprapubic transvesical route (STR) for intraprostatic antibiotic injections and compare it with the transperineal route (TPR), a total of 37 patients suffering from chronic bacterial prostatitis, resistant even to treatment with fluoroquinolones, were randomized to intraprostatic amikacin injections using either STR (n = 19) or TPR (n = 18). Follow-ups were done at weeks 4, 12, 24 and 52. Patients found to have failures at the first follow-up were given an additional injection using the initial route. At the 24th week, 15 patients from both groups were given another injection using the alternative route and were asked to report any subsequent voiding difficulties and compare the discomfort and pain experienced. At the end of 52 weeks, bacteriological cure rates did not differ significantly (44.4 vs. 47.3%). Overall improvement rates in the severity of symptoms and signs were similiar. Considerable difficulty in directing the needle to the prostate due to an excessive amount of subcutaneous fat was experienced, and more than 1 skin puncture was necessary in 5 of the STR group, whereas in the TPR group 7 patients with external hemorrhoids and 1 patient with a rectal fissure had prominent discomfort and pain during the transperineal procedures. Complications such as dysuria or hemospermia were encountered infrequently in both groups, but hematuria was observed more frequently in the STR group (85 vs. 54%). Less discomfort (p < 0.01) and pain (p < 0.01) were reported during access to the prostate by STR, but pain during the injection of the drug did not differ significantly. In conclusion, the percutaneous STR may well be used efficiently and comfortably as an alternative method to TPR when intraprostatic injections are needed in a limited number of cases such as those with a known hypersensitivity to fluoroquinolones or with a history of failure despite long-term systemic treatment with these agents.