The aim of this study was to clarify the clinical significance of bone metabolism in the mandibular condyles in determining condylar resorptive changes. Twelve condyles of patients with idiopathic condylar resorption and degenerative joint disease were analysed using 99mTc HMDP SPECT/CT at baseline and subsequent computed tomography during the follow-up period. Twenty-two healthy condyles were enrolled as controls. After generating three-dimensional SPECT/CT images, two independent observers scored the degree of condylar uptake and measured the morphological changes in the condylar height and condylar volume. In the group with positive condylar uptake, the follow-up computed tomography showed significant decreases in condylar height (-1.69 ± 0.93 mm) and condylar volume (-12.51 ± 10.30%) when compared to healthy controls (condylar height, 0.09 ± 0.54 mm; condylar volume, -0.29 ± 4.22%) (P < 0.001). Moreover, the degree of uptake correlated with the changes in condylar height (observer 1, P = 0.012; observer 2, P = 0.039) and condylar volume (observer 1, P = 0.005; observer 2, P = 0.037). These results suggest that condylar bone metabolism is closely related to the resorptive activity. Thus, SPECT/CT would be useful in the prognostic evaluation or determination of treatment strategies for idiopathic condylar resorption and degenerative joint disease.