© 2015 The Author 2015. Published by Oxford University Press. All rights reserved. Motivation: The transformation of the embryo during development requires complex gene networks, cell signaling and gene-regulated cell behaviors (division, adhesion, polarization, apoptosis, contraction, extracellular matrix secretion, signal secretion and reception, etc.). There are several models of development implementing these phenomena, but none considers at the same time the very different bio-mechanical properties of epithelia, mesenchyme, extracellular matrix and their interactions. Results: Here, we present a new computational model and accompanying open-source software, EmbryoMaker, that allows the user to simulate custom developmental processes by designing custom gene networks capable of regulating cell signaling and all animal basic cell behaviors. We also include an editor to implement different initial conditions, mutations and experimental manipulations. We show the applicability of the model by simulating several complex examples of animal development. Availability and implementation: The source code can be downloaded from: http://www.biocenter.helsinki.fi/salazar/software.html. Contact: Supplementary information: Supplementary data are available at Bioinformatics online.