Design techniques for three-dimensional (3-D) ICs considerably lag the significant strides achieved in 3-D manufacturing technologies. Advanced design methodologies for 2-D circuits are not sufficient to manage the added complexity caused by the third dimension. Consequently, design methodologies that efficiently handle the added complexity and inherent heterogeneity of 3-D circuits are necessary. These 3-D design methodologies should support robust and reliable 3-D circuits, while considering different forms of vertical integration, such as systems-in-package and 3-D ICs with fine grain vertical interconnections. The techniques described in this chapter address important physical design issues and fundamental interconnect structures in the 3-D design process.