The mammalian skull is an informative and versatile study system critical to research efforts across the broad spectrum of molecular, cellular, organismal and evolutionary sciences. The amount of knowledge concerning mammalian skull continues to grow exponentially, fuelled by the advent of new research methods and new material. Computed microtomography, including X-ray imaging using synchrotron radiation, proved to be an important tool for the descriptive and quantitative analysis of cranial anatomy. A major conceptual change, namely combining genetics and development with evolution into ‘evo-devo’ studies, also contributed to our knowledge of the mammalian skull enormously. These advances, coupled with novel techniques now allow researchers to integrate the process of cranial development with data from the fossil record, which is also augmented by seminal discoveries from Africa, Asia and both Americas. However, for decades, there has been no comprehensive source covering fundamental aspects of this vibrant field of evolutionary biology. To address this gap, we offer in this theme issue a balanced mix of research papers and reviews from leading experts in the field and a younger generation of scientists from five continents.This article is part of the theme issue ‘The mammalian skull: development, structure and function’.