The underlying gene interactions that collectively govern the regulation of cellular events can be studied by simultaneous measurement of the levels of mRNA from multiple involved genes. Ideally a single cell should be studied, for comparison with other cells, like and unlike. However, conventional gene expression profiling techniques require several thousands or even millions of cells in order to obtain a sufficient amount of mRNA for analysis. Obtaining this number of cells of a single type is difficult, especially in attempting to study rare stem cells. Single-cell gene expression profiling can, in theory, overcome this limitation. However, conventional analytic methods and equipment are not suitable for analyzing a single-cell, which has a volume of only one or two picoliters. Inexpensive microfluidic devices that can precisely manipulate several nanoliters of fluids are, in theory, ideal for single-cell analysis. By performing biochemical reactions in small volumes, microfluidic devices also minimize material loss in single-cell analysis. This review describes current microfluidic technology applied to single-cell analysis, with a primary focus upon study of single mammalian stem cells. Microfluidic devices have the potential to transform single-cell analysis from a major technological challenge task to a relatively routine procedure for research and clinical assays.