In this study, we try to compare the histological characteristics and the odontogenic capability of apical tissues (AT) at different root development stages of rat molar teeth. AT of mandibular first molars from 8-day-old, 21-day-old, and 35-day-old Sprague-Dawley rats were selected as being representative of root-initiating, root-forming, and root-completing stages, respectively. Cell counting, flow cytometry assays, alkaline phosphatase activity, alizarin red staining, and reverse transcription polymerase chain reaction were performed to assess the proliferation and mineralization potential of apical tissue cells at different stages of root development in vitro. In vivo transplantation of apical tissue cells combined with ceramic bovine bone was used to characterize the differentiation capacity. It was shown that there was a structurally and functionally dynamic change in the apical tissue of developing tooth root of rats, of which the unique developmental potential will reduce gradually with the ending up of root development. The AT of root-initiating and root-forming stage exhibited much higher proliferation and tissue-regenerative capacity than those of root-completing stage. Our present results indicate that the apical tissue, with the sustainable developmental ability throughout almost the whole process of tooth development, can yet be regarded as a competent candidate source for root/periodontal tissues regeneration.