Understanding cellular behavior in both healthy and diseased states requires the ability to molecularly delineate the characteristics of individual cells from complex mixtures. The recent development of cellular microarrays allows such an undertaking. By immobilizing different cell capture and analysis reagents on a solid support, mixtures of cells can be rapidly interrogated for their composition and phenotype. Thus, one can identify and quantitate distinct cell types based on the expression of particular cell surface molecules, as well as analyze their response to defined signals through the secretion of specific factors or other measurable cellular activities. This review focuses on the use of cellular microarrays to detect antigen-specific T cells and their responsiveness, analyze cancer cell types and behavior and to investigate the control of stem cell differentiation.