Recently, Olympus Optical Co. Ltd. has developed a miniaturized device of two-dimensional free flow electrophoresis, and announces it as "microfabricated free flow electrophoresis (mFFE) module". It is significant for efficient design of the module to do numerical simulation of the dynamic behavior in the mFFE process. Thus, we try to do numerical simulation of temperature distribution inside a chamber of the mFFE module, based on the concept of the hybrid model simulation. As to the electroosmotic flow, it is proposed that output of Helmholtz-Smoluchowski equation model updates dynamically the boundary condition (the x-direction velocity of the walls) of the pressure driven flow model by introducing "user-defined functions" in the Fluent 6.0. As results of this hybrid model simulation by using the commercial code, it is confirmed that the simulation method can estimate heterogeneous distributions of temperature inside the mFFE module, which are seen in experimental results. Hence, it is considered that the simulation method is simple and practical for the basic design of the mFFE module. And it is necessary for the detailed design of the module to introduce the models, which are relevant to materials and geometrical structure of the module, into the hybrid model simulation system. (C) 2004 Elsevier B.V. All rights reserved.