The early stages of organogenesis in metazoans differ drastically between higher order taxa such as phyla and classes. The segmented germ band stage in insects, the nauplius stage of crustaceans, and the neurula/pharyngula stage in vertebrates are examples of this diversification. In striking contrast with this divergence, is the similarity of these stages within these taxa, i.e., within insects, crustaceans, and vertebrates. The early stages of organogenesis, or phylotypic stages, have, thus, remained very similar in most species since the evolutionary origin of the taxa. These phylotypic stages are considerably more similar to each other than to the earlier stages of cleavage and gastrulation. Cleavage and gastrulation stages display not only great variability, but also striking examples of apparent convergence among species in different phyla, for example in the many cases of epiblastic cleavage in yolk-rich eggs. This leads to the paradoxical situation that the overall similarity of cleavage and gastrulation stages is in general higher among metazoans than of the early stages of organogenesis, but within phyla and classes the situation is the reverse. We discuss data on cleavage, gastrulation, and early organogenesis and evaluate possible causes for conservation, homoplasy, and diversification in an attempt to throw light on this paradoxical situation. In addition, we discuss a hypothesis that has been proposed to explain the diversity of early stages of organogenesis at the level of metazoans and the similarity within many phyla and classes.