A 72-year-old female received surgical aortic valve replacement for severe aortic stenosis in our hospital. During surgery, black pigmentation was observed in the aortic valve, aorta intima and mitral valve anterior leaflet collocated with calcification. We suspected Alkaptonuria (AKU) as a possible diagnosis for those surgical findings, past medical history and physical findings. A urine test for organic acids showed homogentisic, confirming the diagnosis of AKU. AKU is very rare genetic metabolic abnormality that occurs in about 1 in 25,000 to 100,000 people. AKU involves deficiency in the gene coding for HGA-1,2-dioxygenase, which metabolizes homogentisic acid to maleylacetoacetic acid in the tyrosine metabolic pathway. HGA accumulates in the body, causing black pigmentation in places including the aorta intima and mitral valve.