We report here the adaptation of our electronic microchip technology towards the development of a new method for detecting and enumerating bacterial cells and spores. This new approach is based on the immuno-localization of bacterial spores captured on a membrane filter microchip placed within a flow cell. A combination of microfluidic, optical, and software components enables the integration of staining of the bacterial species with fully automated assays. The quantitation of the analyte signal is achieved through the measurement of a collective response or alternatively through the identification and counting of individual spores and particles. This new instrument displays outstanding analytical characteristics, and presents a limit of detection of approximately 500 spores when tested with Bacillus globigii (Bg), a commonly used simulant for Bacillus anthracis (Ba), with a total analysis time of only 5 min. Additionally, the system performed well when tested with real postal dust samples spiked with Bg in the presence of other common contaminants. This new approach is highly customizable towards a large number of relevant toxic chemicals, environmental factors, and analytes of relevance to clinical chemistry applications.