Abstract CA3D is a simulation program, based on Monte Carlo techniques, which simulates the buffered diffusion of ions in the sub-membrane domain of cells. Two geometries of submembrane domains are considered. The first, a conical domain, applies to spherical cells with a locally uniform distribution of channels while the second, a cylindrical domain, is intended to model ciliar cells and presynaptic terminals. Other domains can be implemented in the code with ease. The entry of ions takes place through discrete entry points (channel pores). Ions diffuse inside the cell and react with endogenous or exogenous buffers, mobile or fixed. The diffusion of ions and binding molecules is modeled as a 3D random walk process by moving each individual ion and molecule. The reaction of ions with the binding molecules is also modeled probabilistically. The outputs of the code are concentration time courses and 2D maps of concentration of ions in the sub-membrane domain of cells.