Heat and fluid flow in microchannels of size (200 mu m x 200 mu m, 5 cm long) of different substrate thicknesses (t = 100 mu m-1000 mu m) and different MEMS (Microelectromechanical Systems) materials (Polyimide, Silica Glass, Quartz, Steel, Silicon, Copper) was studied to observe the effects of thermal conductivity and substrate thickness on convective heat transfer in laminar internal flows. The results of the model were first validated by the theoretical results recommended by standard forced convection problem with H1 (Constant heat flux boundary condition) condition before the results from the actual microchannel configurations were obtained. Thereafter, general Nusselt number results were obtained from the models of many microchannel configurations based on the commercial package COMSOL MULTIPHYSICS (R) 3.4 and were discussed on both local and average basis. A general Nusselt number correlation for fully developed laminar flow was developed as a function of two dimensionless parameters, namely Bi, Biot number and relative conductivity k*, to take the conduction effects of the solid substrate on heat transfer into account. It was also demonstrated when the commonly used assumption of constant heat flux boundary (H1) condition is applicable in heat and fluid flow analysis in microfluidic systems. For this, a new dimensionless parameter was employed. A value of 1.651 for this suggested dimensionless parameter (Bi(0.04)k*(-0.24)) corresponds to 95% of the Nusselt number associated with the constant heat flux boundary condition so that it could be set as a boundary for the applicability of constant heat flux boundary (H1) condition in microfluidic systems involving heat transfer. (C) 2009 Elsevier Masson SAS. All rights reserved.