Three-dimensional heat transfer characteristics and pressure drop of water flow in a set of rectangular microchannels are numerically investigated using Fluent and compared with those of experimental results. Two metamodels based on the evolved group method of data handling (GMDH) type neural networks are then obtained for modelling of both pressure drop (Delta P) and Nusselt number (Nu) with respect to design variables such as geometrical parameters of microchannels, the amount of heat flux and the Reynolds number. Using such obtained polynomial neural networks, multi-objective genetic algorithms (GAs) (non-dominated sorting genetic algorithm, NSGA-II) with a new diversity preserving mechanism is then used for Pareto based optimization of microchannels considering two conflicting objectives such as (Delta P) and (Nu). It is shown that some interesting and important relationships as useful optimal design principles involved in the performance of microchannels can be discovered by Pareto based multi-objective optimization of the obtained polynomial metamodels representing their heat transfer and flow characteristics. Such important optimal principles would not have been obtained without the use of both GMDH type neural network modelling and the Pareto optimization approach. (C) 2007 Elsevier Ltd. All rights reserved.