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OBJECTIVES The study aimed to explore the effects of mouth breathing and hypoxia on the condyle of temporomandibular joint(TMJ) via two animal models. METHODS 24 four-week rats were randomly separated into three groups, consisting of eight control rats, eight intermittent hypoxia (IH) rats and eight intermittent nasal obstruction (INO) rats. We use the IH model and the INO model to simulate children suffering from hypoxia and mouth breathing. After 16 days, the condyle of TMJ and surrounding white adipose tissue (WAT) and skeletal muscle tissue were obtained for further staining and qRT-PCR. Finally, RNA-seq was used to verify the results. RESULTS The intermittent hypoxia cannot significantly change the overall structure in the cause of short-term hypoxia stimulation, but the intermittent nasal obstruction can alter the condyle, WAT and muscle, while also introducing noticeable structural changes in tissue hypoxia and macrophage infiltration. Sequencing data verified these findings and also suggested that this process might involve the Hif-1α/Vegf axis. CONCLUSIONS Our findings reveal the very early structural impact of mouth breathing on condyle reconstruction in rat models, and hypoxia does not induce evident alteration on condyle. However, since these results are mainly focused on rats, further studies are needed to understand its effects on humans.