Heat and fluid flow in a rectangular channel heat sink equipped with longitudinal vortex generators have been numerically investigated in the range of Reynolds numbers between 25 and 200. Aqueous solutions of carboxymethyl cellulose (CMC) with different concentrations (200–2000 ppm), which are shear-thinning non-Newtonian liquids, have been utilised as working fluid. Three-dimensional simulations have been performed on a plain channel and a channel with five pairs of vortex generators. The channels have a hydraulic diameter of 8 mm and are heated by constant wall temperature. The vortex generators have been mounted at different angles of attack and locations inside the channel. The shear-thinning liquid flow in rectangular channels with longitudinal vortex generators are described and the mechanisms of heat transfer enhancement are discussed. The results demonstrate a heat transfer enhancement of 39–188% using CMC aqueous solutions in rectangular channels with LVGs with respect to a Newtonian liquid flow (i.e. water). Additionally, it is shown that equipping rectangular channels with LVGs results in an enhancement of 24–135% in heat transfer performance vis-à-vis plain channel. However, this heat transfer enhancement is associated with larger pressure losses. For the range of parameters studied in this paper, increasing the CMC concentration, the angle of attack of vortex generators and their lateral distances leads to an increase in heat transfer performance. Additionally, heat transfer performance of rectangular channels with longitudinal vortex generators enhances with increasing the Reynolds number in the laminar flow regime.@en