Development of the caudal part of vertebrate embryo occurs when gastrulation is completed and after the regression of the primitive streak. Tail structures form directly from the tail bud blastema, by secondary body development. The caudal part of the body is malformed in splotch and truncate embryos. Splotch is caused by mutation of Pax3 gene and it is characterized by the open neural tube (spina bifida) and defective neural crest migration. Truncate is mutant of Noto gene, characterized by defective development of the notochord. The hypothesis of this study was that the phenotype of splotch and truncate mutants resulted from defective tail bud and secondary body development. The aim of this work was to describe development of the caudal part of C57Bl/6 embryos and to compare it to those of splotch and truncate. Morphology of 9-12.5 days old embryos was investigated by light microscopy using semithin toluidin stained histology sections. The secondary body development in the caudal part of the mouse embryo included gradual differentiation of the tail bud. Tail bud divided and formed the medullary cord and the tail cord. The medullary cord differentiated in the neural tube and the tail cord differentiated in the notochord and the tail gut. Defective neurulation in splotch embryos was not accompanied by defective tail bud morphology, except in 12.5 days old embryos, when complete morphology of the tail, caudal from spina bifida, was disturbed. Spina bifida in splotch embryos developed at the primary and secondary neural tube boundary. In truncate embryos notochord was partially missing. Differentiation of the tail bud was disturbed and the notochord did not develop from the tail cord, but from ventral neuroectoderm. Dorsal part of the tail cord, instead of the notochord, formed additional tail gut. Lack of the notochord was accompanied by disturbed development of the neighboring structures, the neural tube and the somites. Described morphogenetic processes which lead to secondary neural tube and notochord malformations contribute to understanding of human birth defects – spina bifida, caudal disgenesis syndrome and Waardenburg syndrome.