The cytoskeleton is a major determinant of the mechanical strength and morphology of most cells. The composition and assembly state of this intracellular polymer network evolve during the differentiation of cells, and the structure is involved in many cellular functions and is characteristically altered in many diseases, including cancer. Here we exploit the deformability of the cytoskeleton as a link between molecular structure and biological function, to distinguish between cells in different states by using a laser-based optical stretcher (OS) coupled with microfluidic handling of cells. An OS is a cell-sized, dual-beam laser trap designed to nondestructively test the deformability of single suspended cells. Combined with microfluidic delivery, many cells can be measured serially in a short amount of time. With this tool it could be shown that optical deformability is sensitive enough to monitor subtle changes during the progression of cells from normal to cancerous and even a metastatic state. Stem cells can also be distinguished from more differentiated cells. The surprisingly low number of cells required for this assay reflects the tight regulation of the cytoskeleton by the cell. This suggests the possibility of using optical deformability as an inherent cell marker for basic cell biological investigation, diagnosis of disease, and sorting of stem cells from heterogeneous populations, obviating the need for external markers or special preparation. Many additional biological assays can be easily adapted to utilize this innovative physical method. This chapter details the setup and use of the microfluidic OS, the analysis and interpretation of data, and the results of a typical experiment.