Cell analysis and clinical diagnosis systems are now becoming the largest field of application for microchip-based analytical systems. Technological advantages include: small volume, fast analysis time, highly integrated analytical functions, easy operation and small size. For these purposes, basic methodologies for general micro-integration and basic technologies, including fluidic control and ultrasensitive detection, are required. In this review, we introduce our approach to the general integration of various analytical functions and the application of cell analysis systems with cultured cells in microchannels, as well as practical analytical systems for clinical diagnosis utilizing human serum samples.