Germ layers are defined as cell layers that arise during early animal development, mostly during gastrulation, and that give rise to all tissues and organs in adults. The evolutionary origin of the inner germ layers, endoderm and mesoderm, and their relationship have been a matter of debate for decades. In this review we summarize the major modes of endoderm and mesoderm formation found in Metazoa and possible evolutionary scenarios to reconstruct the ancestral state. In the second part, we address the question whether endoderm as well as mesoderm are homologous among Bilateria. In this regard, we propose that the comparative analysis of some crucial transcription factors involved in the early specification and differentiation of these germ layers might provide cues for the level of homology. We focus on four classes of genes: the Zn-finger gene GATA 4-6, the bHLH gene twist, the Krüppel-like Zn-finger gene snail and the T-box gene brachyury. The role of each of these genes in mesendoderm formation is summarized and we propose that the specific function of each of these genes in endoderm and mesoderm formation evolved from the regulation of basic cellular features, such as cell adhesion, cell motility, cytoskeleton and cell cycle.