Calcium pyrophosphate dehydrate deposition disease (CPPDd) is a benign disorder that is typically characterized by excessive presence, crystallization, and deposition of calcium pyrophosphate dehydrate (CPPD) crystals in the synovium, articular cartilage, and surrounding soft tissues. On the other hands, synovial chondromatosis (SC) is also a benign disease that is characterized by synovial tissue that has undergone chondrogenesis and forms cartilaginous nodules that may become loose bodies in the joint space. A 58-year-old Japanese man was referred to our center with a chief complaint of chronic pain in the preauricular region and a 3-year history of trismus. Radiological examination of the affected TMJ revealed chondrocalcinosis. Aspiration of synovial fluid and irrigated the space with pumping procedure were performed in the superior joint space to confirm the diagnosis. However, only synovial tissue was detected, which did not lead to a diagnosis, and there was minimal improvement in his symptoms. We enucleated the tumor by open TMJ surgery. Histopathologically, we diagnosed that coexisting CPPDd and SC in the superior joint space. Our experience showed that “Don't judge a specimen based on the findings of a joint puncture”, and keep in mind that some cases may be coexisting. Improper handling of specimen may result in underdiagnosis.