A heterogeneous interconnect architecture can be a useful approach for the design of 3-D FPGAs. A methodology to investigate heterogeneous interconnection schemes for 3-D FPGAs under different 3-D fabrication technologies is proposed. Application of the proposed methodology on benchmark circuits demonstrates an improvement in delay, power consumption, and total wire-length of approximately 41%, 32%, and 36%, respectively, as compared to 2-D FPGAs. These improvements are additional to reducing the number of interlayer connections. The fewer interlayer connections are traded off for a higher yield. An area model to evaluate this trade-off is presented. Results indicate that a heterogeneous 3-D FPGA requires 37% less area as compared to a homogeneous 3-D FPGA. Consequently, the heterogeneous FPGAs can exhibit a higher manufacturing yield. A design toolset is also developed to support the design and exploration of various performance metrics for the proposed 3-D FPGAs.