The aim of this study was to clarify the pattern of beta cell neogenesis in the alloxan-perfused, beta cells-depleted segment of glucose intolerant mice induced by selective alloxan perfusion. First, duct cells proliferated in the perfused segment, then cells co-expressing multiple islet hormones and transcription factors such as PDX-1, Nkx2.2, Isl1, and Pax6 were observed in duct cells, and newly formed islet-like cell clusters (ICCs) containing beta cells were recognized. In residual beta cell-depleted islets, glucagon or somatostatin and PDX-1 double-positive immature endocrine cells were recognized. Glucagon or somatostatin, insulin and PDX-1 triple-positive cells then appeared and these cells appeared to undergo terminal differentiation into beta cells. In conclusion, we demonstrated at least two different processes of beta cell neogenesis, i.e., formation of new ICCs from ductal epithelium and redifferentiation of residual non-beta islet cells in this model. In addition, transcription factors that appear in the processes of endocrine cell development may also play essential roles during beta cell neogenesis from duct cells.