The presence of urothelial epithelial metaplasia in a seminal vesicle is an exceptionally rare finding. We describe a unique case of urothelial metaplasia of the seminal vesicle and ejaculatory duct, found in a radical prostatectomy specimen from a patient with complex urogenital anatomy. A 70-year-old patient with organ confined (pT2) prostatic adenocarcinoma (Gleason score 3+4 = 7) had a right-sided Hutch diverticulum and a left crossed-fused renal ectopia. Although the histogenesis of urothelial metaplasia in the seminal vesicle remains unclear, in the patient presented herein it likely developed as a consequence of the previously unrecognized malformation.