In this paper, we tested multi-mode optical fibers to select a suitable fiber for effective flow of cell cytometry. In order to align micro nozzle and multi-mode optical fibers, a guide channel was fabricated by silicon wafer etching with MEMS ( Micro Electro-Mechanical System) technologies. The fabricated system is advantageous due to its low cost and simplicity in construction. It is possible because multi-mode optical fibers replace many optical lenses and expensive equipment. As a result of the flow cell cytometry using multi-mode optical fibers for both input and output, it is easy to align and we can reduce power consumption. The sensitivity of the micro flow cell cytometry is much better than other cytometries. The output voltage was as high as 300 mV. We injected various cells through the designed and fabricated flow cell cytometry, and we were able to detect cells. Every cell has its own cellulose and wall which cause different light permeability; therefore, we could get different voltage characteristics according to different cells. From the experimental results, we were able to count the number of cells and differentiate the relative size of the injected cells; therefore, we can use the micro flow cell cytometry for analyzing cells [1, 2]. (C) 2003 Kluwer Academic Publishers.