CellSys is a modular software tool for efficient off-lattice simulation of growth and organization processes in multi-cellular systems in 2D and 3D. It implements an agent-based model that approximates cells as isotropic, elastic and adhesive objects. Cell migration is modeled by an equation of motion for each cell. The software includes many modules specifically tailored to support the simulation and analysis of virtual tissues including real-time 3D visualization and VRML 2.0 support. All cell and environment parameters can be independently varied which facilitates species specific simulations and allows for detailed analyses of growth dynamics and links between cellular and multi-cellular phenotypes.