A 57 years old female complained of severe pain on the right temporomandibular joint (TMJ) area. Her right condyle had been partly resected under surgical operation 13 years ago due to condyle hypertrophy, thereafter she felt dull pain on TMJ area and recently the lesion became severely swelled and painful leading to cancer phobia. The present radiological views showed slightly enlarged and sclerosed condyle with increased radiopacity, but its articular sliding function was almost disable during mouth opening. The patient’s TMJ lesion was carefully managed with conservative physiotherapy and pain treatment. The microsection of condyle head obtained from the previous operation was re-evaluated histologically, and it was finally diagnosed as osteochondrosis dissecans (OCD), exhibiting hyperplastic proliferation of cartilage in condyle head and marked vascular dilatation in epiphyseal zone. This abnormal cartilage tissue was distinguishable from normal cartilage tissue found in the peripheral cartilaginous cap of the same microsection. The involved cartilage cap showed thick hypertrophic chondrocyte zone with horizontal and vertical clefts accompanying diffuse hyaline degeneration. The superficial fibrous zone of cartilage cap was thickened and frequently peeled off, while lower hypertrophic zone of cartilage cap was highly cellular and proliferative. Consequently, the endochondral ossification became aberrant and resulted pre-mature apoptosis of many hypertrophic chondrocytes, followed by diffuse and mild inflammatory reaction in the underlying marrow tissue. Therefore, it was suggested that this hypertrophic condyle lesion, OCD, be differentiated depending on radiological and histological features from ordinary condyle hyperplasia, osteochondroma, and osteoarthritis, and that the pathological confirmation of OCD may provide a reliable modality for dental and medical treatment of chronic and painful TMJ lesion.