Nanobiosensors are an interesting topic of research. However, interfacing with a nanobiosensor requires an analyser system. A number of researchers have proposed different system architecture to interface with nanobiosensors. In this paper, comparison of the existing system architectures for nanobiosensors is discussed. Criteria in designing nanobiosensor system architecture is evaluated, such as the characteristics of the nanobiosensor, a signal processing algorithm, device connectivity, signal interface, processor, data busses and memory requirements. Based on the analysis, an automatic nanobiosensor system architecture is proposed to simplify and accelerate the measurement process.