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This paper presents the architecture for a nanoelectronic logic system in which a regular array of logic gates with programmable interconnections is accompanied by a data transmitter and receiver as well as program registers and a controller. Binary programmable interconnections assure system versatility by providing the means of computing different logic operations. They also allow setting the redundancy level via the number of columns clustered to compute a certain function. A system operation is explained and visualized with a number of examples. The embedded scheme of fault tolerance can effectively mitigate permanent, as well as transient, faults. Some implementation and performance aspects are approached through simulations of single-electron tunneling structures. However, the proposed architectural concept is generic and can be applied to systems implemented with alternative nanotechnologies. Copyright © 2012 John Wiley & Sons, Ltd.