Using backscattered electron (BSE) imaging and scanning electron microscopy, subsequent to a combined treatment of sodium hypochlorite (NaOCl) and ethylenediamine tetra-acetic acid (EDTA) or only with EDTA etching, we observed some structures of non-collagenous calcified matrixes with the aim of revealing the correlation of deposition between calcification degree and organic amount. In human tooth enamel, the NaOCl-EDTA method eroded more intensively the hypocalcified prisms of enamel tufts containing a relatively large amount of EDTA-insoluble organic matter than the hypercalcified normal prismatic enamel containing a small amount of the organic matter. Afibrillar cementum, one of the non-collagenous calcified tissues similar to the enamel, has been reported to consist of organic-rich and poor incremental lamellae. The BSE imaging showed an alternation pattern of hypocalcification and hypercalcification. The hypocalcified lamellae were retained by EDTA etching, while the hypercalcified lamellae showed a resistance against the NaOCl-EDTA method. In the non-collagenous calcareous concretions of human pineal body, organic-rich and poor, and hyper- and hypocalcified incremental lamellae have been reported. The deposition pattern of calcification degree and organic amount was similar to that in afibrillar cementum, and the hypercalcified lamellae showed a resistance against the NaOCl-EDTA method. In conclusion, the high and the lower calcified regions of non-collagenous calcified matrixes contained smaller and larger amounts of EDTA-insoluble organic matter respectively. Moreover, scanning electron microscopy subsequent to the NaOCl-EDTA method corresponding to the BSE imaging clearly showed fine calcified structures compared with the BSE imaging.