—It is generally acknowledged that nanoelectronics will eventually replace traditional silicon CMOS in high-performance integrated circuits. To that end, considerable investments are being made in the research and development of new nanoelectronic devices and fabrication techniques. When these technologies mature, they can be used to create the next generation of electronic systems. Given the intrinsic properties of nanomaterials, such systems are likely to deviate considerably from their predecessors. In this paper, we compare two potential architectures for the design of nanoelectronic FPGAs. By evaluating the performance of nanoelectronic devices at the systems level, we aim to provide insights into how they can be used effectively.1 Keywords-FPGAs; nano-architecture; nanoelectronics; carbon nanotube devices