The present study aimed to clarify the characteristic computed tomography (CT) features that indicate synovial chondromatosis (SC) with a few small calcified bodies or without calcification on panoramic images, and to discuss their differences from the features of temporomandibular disorder (TMD). Panoramic and CT images from 11 patients with histologically verified SC of the temporomandibular joint were investigated. Based on the panoramic images, the patients were classified into a distinct group (5 patients) with typical features of calcified loose bodies and an indistinct group (6 patients) without such bodies. On the CT images, findings for high-density structures suggesting calcified loose bodies, joint space widening, and bony changes in the articular eminence and glenoid fossa (eminence/fossa) and condyle were analyzed. All 5 distinct group patients showed high-density structures on CT images, while 2 of 6 indistinct group patients showed no high-density structures even on soft-tissue window CT images. A significant difference was found for the joint space distance between the affected and unaffected sides. A low-density area relative to the surrounding muscles, suggesting joint space widening, was observed on the affected side in 2 indistinct group patients. All 11 patients regardless of distinct or indistinct classification showed bony changes in the eminence/fossa with predominant findings of extended sclerosis and erosion. Eminence/fossa osseous changes including extended sclerosis and erosion may be effective CT features for differentiating SC from TMD even when calcified loose bodies cannot be identified.