Flow and heat transfer of aqueous based silica and alumina nanofluids in microchannels were experimentally investigated. The measured friction factors were higher than conventional model predictions at low Reynolds numbers particularly with high nanoparticle concentrations. A decrease in the friction factor was observed with increasing Reynolds number, possibly due to the augmentation of nanoparticle aggregate shape arising from fluid shear and alteration of local nanoparticle concentration and nanofluid viscosity. Augmentation of the silica nanoparticle morphology by fluid shear may also have affected the friction factor due to possible formation of a core/shell structure of the particles. Measured thermal conductivities of the silica nanofluids were in approximate agreement with the Maxwell-Crosser model, whereas the alumina nanofluids only showed slight enhancements.Enhanced convective heat transfer was observed for both nanofluids, relative to their base fluids (water), at low particle concentrations. Heat transfer enhancement increased with increasing Reynolds number and microchannel hydraulic diameter. However, the majority of experiments showed a larger increase in pumping power requirements relative to heat transfer enhancements, which may hinder the industrial uptake of the nanofluids, particularly in confined environments, such as Micro Electro-Mechanical Systems (MEMS).