The need for dissipating heat from microsystems has increased drastically in the last decade. Several methods of heat dissipation using air and liquids have been proposed by many studies, and pin-fin micro heat sinks are one among them. Researchers have developed several effective pin-fin structures for use in heat sinks, but not much effort has been taken towards the optimization of profile and dimensions of the pinfin. In this paper the authors studied the effect of different pinfin shapes on the thermal resistance and pressure drop in a specific micro heat-sink. Optimization subjected to two different constraints is studied in this paper. The first optimization is subjected to constant flow rate and the second one is subjected to constant pressure drop. Both optimization processes are carried out using computer simulations generated using COVENTORWARE™. Two of the best structures from each of these optimization studies are selected and further analysis is performed for optimizing their structure dimensions such as width, height and length. A section of the total micro heat-sink is modeled for the initial optimization of the pin-fin shape. The model consists of two sections, the substrate and the fluid. Six different shapes: square, circle, rectangle, triangle, oval and rhombus were analyzed in the initial optimization study. Preliminary tests were conducted using the first model described above for a flow rate of 0.6ml/min. The non dimensional overall thermal resistance of the heat sink, and the nondimensional pumping power was calculated from the results. A figure of merit (FOM) was developed using the nondimensional thermal resistance and nondimensional pumping power for each structure with different pin-fin shapes. Smaller the value of FOM better the performance of the heat sink. The study revealed that the circle and ellipse structures have the best performance and the rectangle structure had the worst performance at low flow rates. At high flow rates rectangular and square structures have the best performance.