Abstract. Micro-flow devices have turned over the years from the subject of fundamental research to fully-fledged industrial applications. Although for some cases the transport phenomena in micro-devices can be handled satisfactorily by using the same approach as for their larger-size counterparts, micro-effects such as electro-osmotic flow (EOF) are typical of small scales and can be employed to circulate coolant through heat sinks by means of electro-osmotic pumping. In order to obey the constraints that different engineering applications impose, design criteria must be employed to optimize the performance of the devices according to the criteria chosen. In this work optimization of the cross-sectional area of a microchannel where EOF and heat transfer at the walls occur is employed to demonstrate how approaches based on the first or second law of thermodynamics may yield opposite results, which are strongly dependent on the peculiarities of EOF, i.e. the ratio of Joule heating to heat transfer at the walls.