Although the large-scale analysis of the human genome has provided a wealth of information for the genetic analysis of cancer and other diseases, most of these advances are unavailable in the clinic due to their expense and complexity. The development of miniaturized devices capable of automated real time analysis of genetic profiles is likely to enable routine genetic analysis of diseases such as cancer, whether for diagnosis or for monitoring treatment throughout the course of the disease. Microfluidic chips allow detection of mutations and abnormal gene expression patterns. Here, we describe the application of microfluidic chips for the molecular monitoring of gene expression profiles associated with human cancer. On-chip RT-PCR products are detectable after as few as 15 cycles of PCR, and from individual cells. On-chip detection is as sensitive as or exceeds the sensitivity obtained using conventional technologies.