The study was designed to investigate calcification in developing rat mandibular bone using whole mount staining, micro-computed tomography (micro-CT) and scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX). Wistar rats at embryonic days 16, 18, and 20 and postnatal weeks 1 and 6 were used. Rats were fixed with 4% paraformaldehyde and heads were resected, frozen and sectioned for histology, then analysed with SEM-EDX. Some of the specimens were observed with micro-CT. Other rats were fixed and stained with alcian blue and alizarin red for whole mount staining. Histology and whole mount staining showed that osteoid was deposited around Meckel's cartilage at day 15 and developed into bone at day 16. Accumulation of Ca and P was identified in the bone matrix with SEM-EDX. The area of bone expanded until week 6. The Ca/P ratio increased, whereas the C/Ca and C/P ratios decreased during development. Micro-CT demonstrated an increase in radio-opacity with bone development. The results suggest that rat mandibular bone formation is initiated around Meckel's cartilage at day 15. Deposition and maturation of the calcium phosphate mineral increase gradually with decrease in the organic component as the rat mandible develops.Rat mandibular bone formation begins with deposition of uncalcified bone matrix in the middle of the mandibular process, lateral to Meckel's cartilage, at embryonic day 15 (E15). The uncalcified bone matrix calcifies at E16 (2,3,13,14). Various regions of the mandibular bone differentiate and expand from the ossification site with time. The mandible has been shown to be one of the first bones to calcify in pigs (6, 10) and rabbits (4). Calcification of the bone matrix in the mandible may proceed by deposition, and then by increase and maturation of calcium phosphate minerals, as reported in calvaria (5). However, little information is available about the process of mandibular bone calcification during development. The study was designed to investigate the process of calcification in developing rat mandibular bone. We examined the developing mandible with histology and whole mount staining to demonstrate the spatiotemporal three-dimensional architecture of developing bone. The process of calcification related to mandibular bone development is shown using micro-computed tomography (micro-CT). Analysis of the concentrations and distributions of elements that constitute the bone matrix, that is, calcium (Ca), phosphorus (P) and carbon (C) is performed by scanning electron microscope equipped with an energy dispersive X-ray spectroscope (SEM-EDX).