Study of thermo-hydraulic characteristics of a novel microchannel heat sink having flow disrupting pins is numerically and experimentally carried out in this paper. Cylindrical pins are inserted from top cover into the rectangular microchannel instead of the conventional technique of pin-fins originating from the base of microchannel. Initially, the effect of pin diameter on the thermo-hydraulic performance is studied and the optimum pin diameter is established, later on thermo-hydraulic performance of pin enhanced microchannel heat sink (PE-MCHS) is compared with conventional microchannel heat sink (MCHS). Of the five pin diameters studied, pin having 0.2mm diameter (relative pin diameter γ=0.4) gives the best performance. Both conventional MCHS and PE-MCHS are subjected to heat flux ranging from 65W/cm2 to 200 W/cm2 and cooled by water flowing at Reynolds number ranging from 745 to 1500. The presence of pins disturbs the velocity distribution completely and increases the heat transfer capacity of the MCHS accompanied by higher pressure drop penalty. The average enhancement factor obtained by this technique is 1.24. Correlations showing the effect of channel width to pin diameter ratio (Wc/ Dp) on Nusselt number (Nu)and friction factor (f) are proposed.