Holt–Oram Syndrome (HOS) is a rare autosomal dominant disorder with an estimated incidence of 1 in 100,000 live births. It is primarily characterized by upper limb deformities and congenital heart defects. Urogenital anomalies are rarely reported in association with HOS. Among them, the coexistence of hypospadias and urethral duplication is extremely uncommon. Urethral duplication results from abnormal embryological development during the third month of gestation, where the urethral folds fail to properly fuse over the urethral plate, potentially resulting in multiple urethral channels or meatuses. We present a rare and complex case of HOS associated with congenital heart anomalies, a permanent cardiac pacemaker, Type IIA2 urethral duplication, and hypospadias, and outline our surgical approach to this unique condition.

A male patient with a known diagnosis of Holt–Oram Syndrome and a permanent cardiac pacemaker presented with a history of urine passage from the ventral side of the penis since birth. Clinical examination revealed one urethral meatus at the subcoronal sulcus and an additional meatus approximately 4 cm proximal to the glans on the ventral aspect of the phallus. Retrograde Urethrography (RGU) and Micturating Cystourethrogram (MCU), confirming Type IIA2 urethral duplication with hypospadias. Surgical intervention included ligation of the proximal dorsal urethra, end-to-end urethroplasty connecting the ventral and dorsal urethras, and a meatoplasty.

The surgical correction was successfully performed without intraoperative or immediate postoperative complications. Postoperative follow-up demonstrated a single functional urethral channel with satisfactory urinary flow through the neomeatus. Cardiac monitoring remained stable throughout, and no pacemaker-related issues were noted during the perioperative period.

This case highlights a rare urogenital presentation in Holt–Oram Syndrome, emphasizing the importance of individualized surgical planning based on anatomical variation. Urethral duplication with hypospadias, though rare, such complex anomalies should be considered in patients with a syndromic presentation. Tailored surgical correction with multi-departmental involvement is the key of success for such complex cases.