Background/PurposeTemporomandibular joint (TMJ) arthritis causes inflammation and degradation of the mandibular condylar cartilage and subchondral bone. Complete Freund's adjuvant (CFA) and collagen-induced arthritis (CIA) are models for studying TMJ arthritis. While micro-computed tomography (micro-CT) is crucial for three-dimensional (3D) bone analysis, it has limitations in imaging nonmineralized tissues. Phosphotungstic acid (PTA) enhances soft tissue contrast. However, research on the 3D imaging of mandibular condylar cartilage and the molecular mechanisms of CFA- and CIA-induced arthritis remains unclear. This study aimed to investigate the bone and PTA-stained cartilage in the mandibular condyle using 3D reconstruction and explore the characteristics of enriched gene ontology terms underlying CFA- and CIA-induced TMJ arthritis in rat models. Materials and methodsRat mandibular condyles were collected from control, CFA, and CIA groups. Live micro-CT created 3D bone structures, and PTA-enhanced micro-CT constructed 3D mandibular condylar cartilage. Gene ontology enrichment analysis identified enriched gene ontology terms from differentially expressed genes through RNA sequencing. ResultsMajor deformities in cartilage volume and bone morphology were observed in the arthritis-induced groups. The CIA group exhibited significant correlations between cartilage volume and bone parameters changes. Gene ontology enrichment analysis indicated fewer terms with upregulated differentially expressed genes related to inflammation and immune response in the CIA group than in the CFA group. ConclusionThis study reveals distinct responses between CFA- and CIA-induced TMJ arthritis models. The CIA group exhibited strong correlations between cartilage volume and bone parameter changes and had less pronounced inflammation and immune response than the CFA group.