Isolating pure stem cell populations is one of the major obstacles in stem cell gene expression profiling due to the lack of stem cell markers. Many results of gene expression profiling studies are difficult to interpret because of the heterogeneous cell populations used in these studies. Single-cell gene expression profiling is perhaps the most attractive gene expression profiling method for studying stem cell gene regulation, because isolating pure stem cell population is not needed. However, current single-cell gene expression profiling methods such as laser capture microdissection (LCM) and patch-clamp analysis lack the high-throughput ability in sample processing. For better understanding of the gene regulation networks during cellular events, a large number of gene expression profiles are required. Therefore, we developed inexpensive microfluidic devices for high-throughput single-cell gene expression profiling. With our devices, cDNA could be obtained from 50 individual cells within 3 hours. This approach can be applied to neural stem cells, and other cell types.