The aim of the study is to determine the characteristics of the material properties of various structures in the temporomandibular joint (TMJ) and the mandibular bone tissues in nanoscopic scale. Using the atomic force microcopy (AFM) with the nanoindentation method, the nanomechanical properties of 6 discs, condylar cartilages and fossate cartilages in the TMJ, and 6 cortical and cancellous bones in the mandible of 3 normal adult men, were measured and analyzed. Results showed that marked differences were found in elastic properties among the different regions of the disc, articular cartilage in the TMJ. In the distribution of elastic modulus in these various structures, the elastic modulus was higher in the anterior and medial regions and lower in the middle, posterior and lateral regions. Otherwise, elastic modulus of the cortical bone in the mandible was approximately 2 times more than the cancellous bone. Elastic modulus in the buccal bone tissues of the mandible was more distinctly below one of the lingual site. The results suggested that the disc, condylar cartilage and fossate cartilage in the TMJ and the cortical and cancellous bone in the mandible were inhomogeneous with the nanolevel measurement. Different structures or various regions in the same structure were loaded by different local mechanical forces in the nanoscale.