In alkaptonuria, the absence of homogentisic acid oxidase (HGO) results in the accumulation of homogentisic acid (HGA) in the body. Associated renal failure is rare and usually occurs in the later stages of the disease. We report a 33-year-old male who presented, initially, with renal failure, but no past history of illness. He had pigmentation of sclerae and ear helices, intervertebral disk calcifications and mild mitral insufficiency. His disease was confirmed by HGA detection in the urine. As size and thickness of renal parenchyma seen on ultrasonography were normal, renal biopsy was performed and it showed glomerular sclerosis, diffuse tubular atrophy and interstitial fibrosis with inflammation. Wall thickening of small arteries and pigment deposits were identified in some kidney tissue elements. He progressed to end-stage renal disease despite supportive therapy.