A microfluidic system and method for employing it to control fluid temperatures of fluids residing within microchannels of a microfluidic device. The microfluidic device is provided with a top layer and a bottom layer and microchannels configured therebetween. Temperature of the fluid within the microchannels is controlled in various ways including the use of electrical resistive heating elements and by providing zones located in contact with the top and bottom layers of the microfluidic device for circulating heat transfer of fluid therein.