Flow cytometry has been widely employed to count, sort and analyze various characteristics of cells since its discovery, and has made significant contribution to the development of biology, pharmacology and medicine in recent decades. As a complicated instrument, a typical flow cytometer consists of three subsystems: fluidic, optical and electronic, where the optical subsystem is often regarded as the heart. In this presentation, we will focus on the optical part of the flow cytometer and discuss how to select the right components to maintain the optical alignment accuracy and stability, and thus to boost the performance of the whole equipment. Featured MKS products and solutions that are critical to the performance of a flow cytometry instrument including mirror mounts, optics, stages will also be introduced during the presentation.