Ochronosis is a rare autosomal recessive metabolic disease caused by homogentisic acid oxidase enzyme deficiency. High homogentisic acid levels will eventually result in black deposits in skin, sclerae, connective tissues and urine (alkaptonuria). It can lead to early degeneration of connective tissues and cartilage. Ochronosis can damage normal cartilage, leading to secondary osteoarthritis. The diagnosis is often delayed because of its low prevalence and non-specific early symptoms. In our patient, the secondary osteoarthritis due to ochronosis deposits in the cartilage was treated by total knee arthroplasty, with good clinical outcome. This article reports the first case of ochronosis with secondary osteoarthritis of the knee in a patient previously diagnosed with cryptogenic organising pneumonia (COP).