Background Ductus deferens may manifest in a variety of anomalies such as its absence, duplication, ectopy, or diverticulum. Ectopic seminal tract opening has two main types, ectopic ejaculatory duct opening, and ectopic vas deferens opening. Generally, ductus deferens anomalies affect approximately 0.05% of the population. Patients may be asymptomatic or complaining of urinary tract infections and/or epididymitis. Most of these cases are associated with renal dysplasia. To confirm the diagnosis Cystourethroscopy catheterization and retrograde urethrogram should be performed, but the definitive diagnosis is done by vasography. The definitive treatment is complete surgical resection of the pathological urogenital connection. This case is commonly discovered while exploring other findings such as testicular torsion and inguinal hernia. Case presentation We report a rare case of an 11-year-old male who presented with gross hematuria and numerous congenital malformations including a left polydactyly clubfoot, polyorchidism, with several surgical procedures, and left kidney dysgenesis. Surgery was performed for a left inguinal hernia, during which a third undescended testicle was discovered incidentally and was eradicated. A retrograde urethrogram was performed to establish the diagnosis. A fistula- that is connected with the left ureter- was resected. The histopathologic findings confirmed the diagnosis of true duplication of the Vas deferens, with communication between the ureter and the vas deferens. By follow-up, the kidney function tests were within normal limits. Conclusions This case report aims to highlight the early diagnosis and management of the duplicated vas deferens and the associated congenital malformations to improve the prognosis and kidney function and to avoid long-term complications.