We report about a 78-year-old woman with severe aortic valve stenosis (AS). She had heavily calcified and thickened aortic valve leaflets with black pigmentation. After excision of the aortic valve leaflets, biological aortic valve replacement (AVR) was performed. Alkaptonuria was diagnosed and confirmed based on increased urinary excretion of homogentisic acid. She has had no cardiovascular system-related symptoms for 3 years and no evidence of structural valve deterioration. Data on the long-term outcomes of AVR associated with structural valve deterioration that could regulate prosthetic valve selection in alkaptonuria are limited. Therefore, further research on the natural evolution of AS and the rate of structural valve deterioration after AVR is needed to provide an optimal prosthesis for these patients.