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Branchio-oto-renal (BOR) syndrome is an autosomal dominant disorder characterized by the coexistence of branchial cysts or fistulae, external ear malformation with pre-auricular pits or tags, hearing impairment and renal malformations. However, the presence of the main features varies in affected families. Here, we present a 16-year-old boy admitted to the Department of Nephrology at the Pediatric Clinic, University Clinical Center of Kosovo, Pristina, Republic of Kosovo because of severe renal insufficiency diagnosed 6 years ago, which progressed to end-stage renal failure. Clinical examination on readmission showed a pale, lethargic and edematous child, with auricular deformity, pre-auricular tags and pits as well as bilateral branchial fistulae. Laboratory tests revealed high blood urea nitrogen (BUN) 15.96 mmol/L and serum creatinine 633.0 µmol/L; low glomerular filtration rate (GFR) 12 mL/min./ 1.73 m2 and massive proteinuria 4+. Abdominal ultrasound showed bilateral kidney hypoplasia. A novel mutation of the EYA1 gene was confirmed. Daily hemodialysis is continuing until renal transplantation is done. This case is presented to increase awareness among general practitioners to consider BOR syndrome or other renal abnormalities in patients with branchial fistula and/ or external ear anomalies or similar findings in other family members.