Our research on the evolution of the vertebrate head focuses on understanding the developmental origins of morphological novelties. Using a broad comparative approach in amphibians, and comparisons with the well-studied quail-chicken system, we investigate how evolutionarily conserved or variable different aspects of head development are. Here we review research on the often overlooked development of cranial muscles, and on its dependence on cranial cartilage development. In general, cranial muscle cell migration and the spatiotemporal pattern of cranial muscle formation appears to be very conserved among the few species of vertebrates that have been studied. However, fate-mapping of somites in the Mexican axolotl revealed differences in the specific formation of hypobranchial muscles (tongue muscles) in comparison to the chicken. The proper development of cranial muscles has been shown to be strongly dependent on the mostly neural crest-derived cartilage elements in the larval head of amphibians. For example, a morpholino-based knock-down of the transcription factor FoxN3 in Xenopus laevis has drastic indirect effects on cranial muscle patterning, although the direct function of the gene is mostly connected to neural crest development. Furthermore, extirpation of single migratory streams of cranial neural crest cells in combination with fate-mapping in a frog shows that individual cranial muscles and their neural crest-derived connective tissue attachments originate from the same visceral arch, even when the muscles attach to skeletal components that are derived from a different arch. The same pattern has also been found in the chicken embryo, the only other species that has been thoroughly investigated, and thus might be a conserved pattern in vertebrates that reflects the fundamental nature of a mechanism that keeps the segmental order of the head in place despite drastic changes in adult anatomy. There is a need for detailed comparative fate-mapping of pre-otic paraxial mesoderm in amphibians, to determine developmental causes underlying the complicated changes in cranial muscle development and architecture within amphibians, and in particular how the novel mouth apparatus in frog tadpoles evolved. This will also form a foundation for further research into the molecular mechanisms that regulate rostral head morphogenesis. Our empirical studies are discussed within a theoretical framework concerned with the evolutionary origin and developmental basis of novel anatomical structures in general. We argue that a common developmental origin is not a fool-proof guide to homology, and that a view that sees only structures without homologs as novel is too restricted, because novelties must be produced by changes in the same framework of developmental processes. At the level of developmental processes and mechanisms, novel structures are therefore likely to have homologs, and we need to develop a hierarchical concept of novelty that takes this into account.