This paper deals with the dynamic simulation of chromatographic processes using MATLAB. Three different simulation tools are presented,; BIOPRO2, CPS toolbox and an application using of FEMLAB. Our main application is separation of biomolecules, like proteins, using different kinds of stationary phases. BIOPRO2 has a user-friendly graphical interface and is mainly based on simplified models for fast simulation. The CPS toolbox can facilitate the development of a simulation of different classes of models based on a number of simulation methods. FEMLAB is a general modelling and simulation system based on finite element method.