Abstract-As silicon circuits quickly approach their physical limitations, researchers are actively looking for novel building blocks to develop nanocircuits. However, future nanoelectronic circuits are more error-prone than conventional CMOS designs because of their self-assembly design. To help design fault-tolerant nanoscale circuits, new circuit design and testing tools are needed. In this paper, an efficient methodology to evaluate nanoscale circuit fault tolerance based on Belief Propagation (BP) algorithm is proposed. Compared with existing approaches, the BP algorithm is more efficient in terms of memory requirements and CPU times. The proposed methodology can be easily run on multiple CPUs to achieve parallel processing and thus further reduces simulation time.