There are three germ layers in vertebrate embryo: Ectoderm, Endoderm and Mesoderm. They differentiate in a programmed manner during development starting with an undifferentiated ball of cells known as morula stage of human embryo. It is an enormous question where the answer could be an entire book of developmental biology! In mice there are mutants that affect mesoderm differentiation, human trisomies show multiple developmental defects during differentiation as well as organogenesis. Some of these defects involve germ layers while others include tissue formation from germ layers. Hope this helps.
