Abstract This paper presents a numerical study of laminar forced convection in heat sinks with micro pin-fin structure. A water cooled heat sink on a 1 cm × 1 cm substrate has been studied. Both pin-finned microchannel heat sinks (MCHSs) and pin fin heat sinks (PFHSs) are investigated. The distribution patterns of the fabricated pin-fins are either oblique or staggered. The Navier–Stokes and energy equations for the liquid region and the energy equation for the solid region are solved simultaneously to find the hydraulic and heat transfer performance of the heat sinks. The heat removal fluxes in finned MCHSs and PFHSs with different height of micro pin fins are compared with that in an optimum simple MCHS in equal pumping powers. It is shown that for the same pumping powers, the heat removal of the finned heat sinks is lower than that in the optimum simple MCHSs at medium and high pumping powers. The finned heat sinks, however, perform slightly better than an optimum simple MCHS for small pumping powers. It is also shown that studied heat sinks can be optimized using entropy generation minimization.