This special issue of The Anatomical Record presents a series of papers that apply the method of finite element analysis (FEA) to questions in vertebrate biomechanics. These papers are salient examples of the use of FEA to test hypotheses regarding structure-function relationships in complexly shaped biological objects such as skulls and in areas of the skeleton that are otherwise impervious to study. FEA is also a powerful tool for studying patterns of stress and strain in fossil animals and artificial constructs hypothesized to represent ancestral conditions. FEA has been used deductively, to study patterns of growth and development, and to investigate whether skull shapes can be created from amorphous blocks using an iterative approach of loading and removing elements. Several of the papers address methodological issues, such as the relative importance of loading conditions and material properties for generating an accurate model and the validation of models using in vivo strain data. Continuing improvements in model building techniques will make possible increased application of FEA to study the functional effects of variation in morphology, whether through ontogenetic or phylogenetic transformations.