MicroRNAs (miRNAs) are a class of 17–25 nt non-coding RNAs that have been shown to have critical functions during development in a wide variety of biological processes, including cell cycle regulation, cell differentiation, apoptosis, maintenance of stemness and imprinting (Ambros, 2004; Alvarez-Garcia and Miska, 2005; Harfe, 2005; Plasterk, 2006). Profiling of miRNAs is a prerequisite for dissecting their biological function. A number of methods have been developed for this purpose, such as the miRNA microarray techniques during the past three years (Krichevsky et al., 2003; Babak et al., 2004; Barad et al., 2004; Calin et al., 2004; Liu et al., 2004; Miska et al., 2004; Nelson et al., 2004; Sempere et al., 2004; Sioud and Rosok, 2004; Sun et al., 2004; Thomson et al., 2004; Baskerville and Bartel, 2005; Liang et al., 2005; Lu et al., 2005; Castoldi et al., 2006; Neely et al., 2006). Most of these methods need microgram (µg) amounts of total RNA for the assay, although a few of them are more sensitive and only need nanogram (ng) amounts of RNA. However, all of the methods require purification of total RNA for the assays, which is not feasible for single cell miRNA expression profiling. In some cases, such as the analysis of very early embryos, adult stem cells, and cancer stem cells, it is often crucial to analyze miRNA profile in individual cells. In these cases, very limited amounts of material may be available for miRNA profiling assay.