The present invention generally relates to design automation techniques and more particularly to the design of customized microfluidic systems using a microfluidic computer aided design system. In one embodiment of the present invention the system includes a synthesis module for synthesizing software of a design into a component level description of the design. The design has a plurality of microfluidic components, and the component level description has symbols associated with the plurality of microfluidic components. The system further includes a design capture module, including a schematic entry tool, for placing and connecting the symbols on a schematic according to the design; and a functional analysis module for functionally simulating selected symbols of the schematic.