In this paper the authors are studying the effect of introducing S-shaped pin-fin structures in a micro pin-fin heat sink to enhance the overall thermal performance of the heat sinks. For the purpose of evaluating the overall thermal performance of the heat sink a figure of merit (FOM) term comprising both thermal resistance and pumping power is introduced in this paper. An optimization study of the overall performance based on the pitch distance of the pin-fin structures both in the axial and the transverse direction, and based on the curvature at the ends of S-shape fins is also carried out in this paper. The value of the Reynolds number of liquid flow at the entrance of the heat sink is kept constant for the optimization purpose and the study is carried out over a range of Reynolds number from 50 to 500. All the optimization processes are carried out using computational fluid dynamics software CoventorWARE™. The models generated for the study consists of two sections, the substrate (silicon) and the fluid (water at 278K). The pin fins are 150 micrometers tall and the total structure is 500 micrometer thick and a uniform heat flux of 500KW is applied to the base of the model. The non dimensional thermal resistance and nondimensional pumping power calculated from the results is used in determining the FOM term. The study proved the superiority of the S-shaped pin-fin heat sinks over the conventional pin-fin heat sinks in terms of both FOM and flow distribution. S-shaped pin-fins with pointed tips provided the best performance compared to pin-fins with straight and circular tips.