Purpose In recent years, many studies have made considerable progress in the development of stem cell-based therapies for Hirschsprung’s disease (HD). However, the question of whether enteric neural crest-derived cells (ENCCs) that are transplanted into aganglionic gut can migrate, proliferate and differentiate in a normal manner remains unanswered. Thus, we designed this study to compare the behavior of ENCCs transplanted into the aganglionic gut of endothelin receptor B knockout (Ednrb-KO) mice versus wild-type (WT) mice. Methods ENCCs were isolated from the fetal guts of Sox10 transgenic mice, in which ENCCs were labeled with an enhanced green fluorescent protein, Venus, on embryonic day 18.5 (E18.5). Neurospheres were generated and transplanted into the aganglionic region of either Ednrb-KO mice gut, or WT mice gut that had not yet been colonized, on E12.5. Time-lapse imaging of the transplanted ENCCs was performed after 24h, 48h and 72h of culture. Neuronal differentiation was evaluated using whole-mount immunohistochemistry. Results Sox10-positive ENCCs were seen to successfully migrate into the myenteric region of the aganglionic gut following transplantation in both the Ednrb-KO and WT mice. The ratio of Tuj1-positive/Sox10-positive cells was significantly increased after 72h of culture compared to 24h in the Ednrb-KO mice, which suggests that the transplanted ENCCs differentiated over time. In addition, at the 72h timepoint, neuronal differentiation of transplanted ENCC in the aganglionic gut of Ednrb-KO mice was significantly increased compared to that of WT mice. Conclusions The results of our study demonstrated that transplanted ENCCs migrated into the myenteric region of aganglionic recipient gut in mice. The increased neuronal differentiation of transplanted ENCC in Endrb-KO mice gut suggests that the microenvironment of this region affects ENCC behavior following transplantation. Further research to explore the characteristics of this microenvironment will improve the potential of developing cell therapy to treat HD patients.