Alkaptonuria is a rare inherited disease resulting from a genetic variant leading to homogentisic acid accumulation in body tissues, causing a broad spectrum of symptoms. Our case involves a Caucasian male diagnosed in his 70s, who shares a constellation of symptoms and the diagnosis with his monozygotic twin brother. The symptoms include early-onset arthropathy, tendinopathy, osteopenia, discolouration of the auricular regions and fingers, scleral discolouration, secondary glaucoma, proteinuria, calcification of the mitral valve and black urethral and prostate stones. Additionally, the patient suffers from chronic cough, polyneuropathy and corpus cysts in the thoracic spine have been found. This case highlights the importance of holistic assessments, recognition of familial symptom patterns and early identification of key clinical indicators for rare disease diagnosis. It also underscores the challenge of differentiating rare symptomatic manifestations from those unrelated to alkaptonuria.