In this work effects of adding vortex generators to multilayer micro channels were studied. In order to study the effect of heat transfer and pressure drop of vortex generators, different types of generators were compared. Examination of the results showed that the best performance were obtained from two types of vortex generators; i.e. a V-type with 45 degree vortex generator facing the flow and a delta wing vortex generator of first kind again facing the flow. In the next step, flow behavior and heat transfer in a single layer and also in a two layer micro channel with counter flow in the layers without vortex generator were studied. And finally the effect of adding V-type vortex generators and delta Wing of first kind both facing to the flow a single layer and also in a two layers micro channel were investigated. In these studies parameters such as local Nusselt number, friction factor, performance coefficient, maximum temperature of the electronic device and total thermal resistant were studied. Results show that at similar Raynolds number, total thermal resistant of a two layer counter flow micro channel is half of a single layer micro channel. By adding vortex generators to a single layer micro channel, the maximum temperature of the electronic device and total thermal resistant will decreased as the mean Nusselt number, friction factor and performance coefficient increase. Performance of a two layer micro channel with V-type vortex generator is better than a two layers micro channel with a delta wing type vortex generator at the same height and Reynolds number. Key words Micro channel, Vortex generator, Heat transfer, Performance coefficient.