Background: In juvenile idiopathic arthritis involvement of the temporomandibular joints (TMJs) is often associated with severe mandibular growth deviations. The relation between condylar growth deviations, inflammation severity, the micro-architectural composition, and the bone quality has not previously been investigated. Aim: We studied the effects of antigen-induced arthritis on the bony structures in rabbit mandibular condylar development, in particular the morphological changes and the bone micro-architecture. Materials and Methods: Included were juvenile rabbits with ovalbumin-induced TMJ arthritis treated with intraarticular saline, intra-articular etanercept (an anti-TNF-α drug) or subcutaneous etanercept. One TMJ from each animal was scanned using micro-computed tomography and structural parameters were calculated. Three-dimensional reconstructions of the mandibular condyle were scored blindly by two independent observers as normal or abnormal. TMJs were stratified for condylar morphology and evaluated against data on inflammation, trabecular structural parameters, and overall mandibular growth. Mineral apposition rate was measured using fluorochrome labelling. Results and discussion: Abnormal morphology was seen in 15 of 32 animals available for data analysis and was strongly related to the degree of inflammation. However, no differences in trabecular structural parameters or mineral apposition rate were seen according to treatment. Erosions were an uncommon finding. Abnormal condylar morphology was not associated with overall mandibular growth. Conclusion: We show that severe inflammation in the TMJs during mandibular development is associated with morphological changes of the mandibular condyle. Morphological changes may occur because of deficient development of condylar cartilage and not because of resorptions in times of active inflammation, and is hence a temporary phenomenon.