This study aimed to investigate whether transurethral alprostadil could be used for the diagnosis of erectile dysfunction using colour duplex ultrasound. The ultrasonography results were compared after transurethral and intracavernous alprostadil administration in 20 patients with erectile dysfunction. There were no significant differences in the mean peak systolic velocities (PSVs) between the two routes of administration, but the mean end diastolic velocities (EDVs) showed significant differences, with patients treated with transurethral alprostadil having higher EDVs. Linear regression analysis of the PSVs reached following the two routes of administration showed a moderate relationship, but linear regression analysis of the EDVs showed no relationship. We concluded that transurethral alprostadil was an inappropriate vasoactive drug to use with colour duplex ultrasonography for the evaluation of patients with erectile dysfunction because it required a longer scan time and it was less effective and less reliable than intracavernous alprostadil at stimulating complete corporeal smooth muscle relaxation.