Our planet’s biodiversity is the result of countless evolutionary radiations across a wide range of temporal, geographical and taxonomic scales. Adaptive radiation is the extensive and often rapid evolution of morphologically and ecologically diverse species from a single ancestor. It usually implies two coincidental processes: multiplication of species number (species richness) and increased phenotypic disparity (morphological diversification). The exact mechanisms underlying such taxonomic and morphological diversifications are still being explored and described. Some of the most important examples of adaptive radiations representing different vertebrate clades and taxonomic levels are Darwin’s finches (Thraupidae), New World leaf nosed bats (Phyllostomidae) and crocodilians (Crocodylia). Cranial diversity in vertebrates is a particularly inviting research topic for understanding mechanisms for adaptive radiations as animal heads and faces show many dramatic and unique adaptive features, which reflect their natural history. We aim to reveal molecular mechanisms underlying evolutionary processes that generate such morphological variation. To this purpose, we employ a synergistic combination of geometric morphometrics, comparative molecular embryology and functional experimentation methods to trace cranial evolution in reptiles, birds and mammals, some of the most charismatic animals on our planet. Our research on morphological skull and face diversity in birds, crocodilians and bats is revealing how particular changes in development, such as heterochrony, can produce morphological alterations for natural selection to act upon. We also show that cranial morphological diversification observed in adaptive radiations can be explained by differential growth and underlying dynamic patterns of cell proliferation and differentiation during craniofacial morphogenesis.