Our previous study showed that mouse neural crest cells (NCCs) from the sacral level were able to migrate from the dorsal neural tube over long distances to enter the hindgut. In the present study, we sought to determine whether Sox10 mutation affected the migration of sacral NCCs prior to their entry to the hindgut. Dominant megacolon (Dom) mice with a spontaneous mutation of Sox10, and experimental techniques including cell labelling, whole embryo culture and multiple immunohistochemical staining were used. We found that in wild type embryos, sacral NCCs caudal to somite 24 began their migration from the neural tube at E9.5, started to aggregate on two sides of the hindgut to form pelvic ganglia at E11.5 and by around E14.0 entered the hindgut at S2 and S3 vertebral levels. In Sox10Dom heterozygous mutants, sacral NCCs migrated along the same spatio-temporal pathway, although the number of migrating sacral NCCs was significantly reduced. In Sox10Dom homozygotes, the number of migrating sacral NCCs was further reduced and no NCCs reached the pelvic ganglia region. TUNEL assay did not reveal any significant increase in sacral NCC death in either Sox10Dom/+ or Sox10Dom/Dom mutants. Our observations indicate that the Sox10 mutation in Dom embryos affects the migration of sacral NCC before they enter the hindgut by reducing the number of migrating sacral NCCs.