It can be difficult for researchers and clinicians to evaluate bone tissues after some regenerative bone treatments because bone is always undergoing the process of remodeling. Moreover, hard tissues such as bone or teeth are typically very difficult to handle to prepare fresh and proper materials for clinical use. Therefore, regenerative bone tissues must be evaluated by adequate methods. In our previous studies, we developed a bone regeneration system using a combination of a non-viral bone morphogenetic protein gene-expression plasmid vector and in vivo electroporation. Using a model of ectopic bone formation in the skeletal muscles of rats made it easy to evaluate the bone-inductive potential of our developed system. In this study, we used bone morphometry analysis to evaluate the alveolar bone with our gene-transfer system. Upon labeling alveolar bone with calcein and tetracycline in rats and analyzing double-staining, we concluded that histomorphometry analysis is an efficient method for evaluating alveolar bone regeneration induced by a combination of non-viral plasmid vector and in vivo electroporation.