Aims:  To develop a miniaturized analytical system for counting of bacteria. Methods and Results:  Escherichia coli cells were used throughout the experiments. The system consists of a microfluidic chamber, a fluorescence microscope with a charge‐coupled device (CCD) camera and syringe pumps. The chamber was made of a silicone rubber (30 × 30 mm and 4 mm high). The E. coli cells were flowed from a micro‐nozzle fabricated in the chamber and detected with the CCD camera. The individual cells were indicated as signal peaks on a computer. The cell counts showed a good correlation compared with that of a conventional plate counting method, and results of the simultaneous detection of live and dead cells were also presented. Conclusions, Significance and Impact of the Study:  The system having a small disposable nozzle has the advantages for low cost and safe medical or environmental analysis, when compared with a conventional flow cytometer. This is the first step of the development of a one‐chip microbe analyzer.

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