This study presents a new micromachine-based cell counting and sorting system capable of multi-wavelength detection for biological applications. Chip-based flow cytometers have been extensively investigated recently. Several unique features have been integrated on this new cell-analysis system. First, a series of new serpentine-shape pneumatic micro-pumps were used to drive sample and sheath flows and generate a hydrodynamic focusing effect. The control of fluids could be achieved with ease by using this approach. Multiple embedded optical fibers were then used to transmit the light source and collect induced fluorescence signals in and out of the chip device. Cells labeled with different fluorescent dyes could be then individually detected by corresponding fibers using lasers with different wavelengths. Finally, three pneumatic micro-valves downstream were used for cell sorting. The developed micro flow cytometer could be used for fast analysis of cell-related bio-medical applications.