Probing interactions of biological systems at the molecular level is of great importance to fundamental biology, diagnosis, and drug discovery. A rational bioassay design of lithographically integrating individual point scattering sites into electrical circuits is capable of realizing real-time, label-free biodetection of influenza H1N1 viruses with single-molecule sensitivity and high selectivity by using silicon nanowires as local reporters in combination with microfluidics. This nanocircuit-based architecture is complementary to more conventional optical techniques, but has the advantages of no bleaching problems and no fluorescent labeling. These advantages offer a promising platform for exploring dynamics of stochastic processes in biological systems and gaining information from genomics to proteomics to improve accurate molecular and even point-of-care clinical diagnosis.