This study was designed to search for regulatory matrix proteins in bone and tooth calcification that are degenerated by MMP-2 (Matrix Metalloproteinase-2). The concentration of elements of calcium, phosphorus and carbon was compared between MMP-2 deficient mice (MMP-2 KO) and wild type mice (WT) to understand how deficiency in MMP-2 affects composition of the elements and how the element composition is involved in calcification. Tibiae of MMP-2 KO and WT at 7 weeks were examined with micro-computed tomography, scanning electron microscope with energy dispersive X-ray spectroscopy and histology. The bone mineral density of the cortical bone in tibiae were lower in MMP-2 KO than WT. In contrast, no significant difference was recognized in composition of the elements or in histological observation.