The progress in microfabrication and lab-on-a-chip technologies has been a major area of development for new approaches to bioanalytics and integrated concepts for cell biology. Fundamental advances in the development of elastomer based microfluidics have been driving factors for making microfluidic technology available to a larger scientific community in the past years. In line with this, microfluidic separation of cells and particles is currently developing rapidly where key areas of interest are found in designing lab-on-a-chip systems that offer controlled microenvironments for studies of fundamental cell biology. More recently industrial interests are seen in the development of micro chip based flow cytometry technology both for preclinical research and clinical diagnostics. This critical review outlines the most recent developments in microfluidic technology for cell and particle separation in continuous flow based systems. (130 references).