Congenital malformations of the seminal vesicles (SVs) are rare and are often associated with abnormalities of the ipsilateral upper tracts as embryologically both the ureteral buds and SVs arise from the mesonephric ducts. The triad of SV cysts, ipsilateral renal agenesis, and ejaculatory duct obstruction is known as the Zinner syndrome. We herein present the case of Zinner syndrome with hematuria as the mode of presentation. A 52-year-old gentleman presented with complaints of gross and painless hematuria for 3 months. An initial ultrasound revealed absent right kidney with a cystic structure abutting the urinary bladder. Cystoscopic examination revealed a high bladder neck. Magnetic resonance imaging of the abdomen revealed an absent right kidney and a large tubular structure in the region of the right ureter extending up to right SV with blood content and stones within. It was distally seen communicating with one of the cysts of the right SV. The cystic structure was removed with a robot-assisted laparoscopic approach. The console time was 110 min with minimal blood loss. Postoperative course was uneventful. Histopathology of the cyst wall revealed chronic inflammation. The patient is doing well on 6 months follow-up. This case was unique in terms of it presenting with a large intra-abdominal cyst with sharp stones within, probably first of its kind to be ever reported. Surgery is mandated for such symptomatic cysts and the daVinci robot with its minimally invasive approach offers the perfect platform for treating such challenging cases.