Seminal vesicle cysts are rare lesions and usually asymptomatic. However, when symptoms occur it is typically during the early sexually active period. Furthermore, seminal vesicle abscesses (SVAs) are extremely rare and often difficult to diagnose due to the absence of any typical clinical signs. We herein describe a 2-month-old boy with a left SVA and ipsilateral multicystic dysplastic kidney (MCDK) who presented with a recurrent urinary tract infection (UTI). Magnetic resonance imaging proved to be a valuable diagnostic tool in our patient. Percutaneous transrectal puncture and aspiration were performed, because of recurrent UTI when intravenous antibiotic therapy had been stopped. Three weeks after the procedure, however, the SVA recurred, and, therefore, a transperitoneal laparoscopic excision of the left SVA, ureteral remnant and dysplastic renal tissue was performed. To the best of our knowledge, this is the first case of infantile SVA associated with ipsilateral MCDK. Pediatric clinicians should consider this urological anomaly in boys presenting with intractable UTI, although it is extremely rare.