A case of CA19-9-producing seminal vesicle cyst with ipsilateral renal agenesis is reported. A 29-year-old man was admitted to our hospital for perineal pain and urinary retention. Digital rectal examination revealed a large soft mass that fluctuated in the area of the prostate and seminal vesicles. Magnetic resonance imaging revealed a right kidney defect, and ipsilateral dilation and cystic enlargement of the right seminal vesicle. Transrectal puncture of the seminal vesicle cyst was performed. The contents were pus and old red blood cells. Initially, the serum CA19-9 level was extremely high (145.8 U/ml) but was normalized by the treatment with antibiotics after the puncture. The symptoms subsided without recurrence.