Alkaptonuria is a genetic disorder characterized by an accumulation of homogentisic acid due to an enzymatic defect of homogentisate 1,2 dioxygenase. The homogentisic acid is excreted exclusively by both glomerular filtration and tubular secretion leading to the renal parenchyma being exposed to high concentrations of homogentisic acid. The alkaptonuric patients are at higher risk of renal stones (and of prostate stones for males), usually in the later stages of the disease. We describe the case of a 51-year-old man whose renal and prostate stones were analyzed by X-ray diffraction and infrared spectroscopy, respectively. We review the cases of alkaptonuria (AKU) patients reported in the literature for whom the composition of kidney or prostate stones was assessed with physical or chemical techniques. In this paper, we also discuss the advantages and drawbacks of the different methodologies.