Seminal vesicle cysts combined with genitourinary anomalies are uncommon. We present a 43-year-old married man who suffered from difficulty in urination and irritating voiding symptoms for 3 years. The symptoms worsened in the last 6 months. Digital rectal examination revealed a palpable large soft mass behind the prostate. Diagnostic imaging showed a left seminal vesicle cyst with an intravesical protrusion. The ipsilateral kidney and ureter were absent. Transrectal aspiration of the cyst was performed, which improved the clinical genitourinary symptoms. The maximal and mean urinary flow rates increased from 18 to 37 mL/s and from 6 to 16 mL/s, respectively.