Ventral furrow formation is the first large-scale movement in the Drosophila cellular blastoderm which involves the co-ordinated shape change of cells, and as such is an ideal system to use as a proof of principle for simulation methods to study the mechanics of morphogenesis. We have developed a 3D finite element method model of ventral furrow formation by decomposing the total deformation into two parts: an imposed active deformation, and an elastic passive deformation superimposed onto the latter. The model imposes as boundary conditions (i) Vito, C., Muñoz, J.J., Miodownik M., A 3D finite element model of ventral furrow invagination in the Drosophila melanogaster embryo, Journal of the Mechanical Behavior of Biomedical Materials, Vol. 1, Issue 2, pp. 188-198, 2008 compared the model with a 2D model and shown that it exhibits a more robust invagination phenomenon. The 3D model has also revealed that invagination causes a yolk flow from the central region to the anterior and posterior ends of the embryo, causing an accordion-like global compression and expansion wave to move through the embryo. Such phenomenon cannot be described by 2D models.