Analysis of RNA expression levels by real-time reverse-transcription (RT) PCR has become a routine technique in diagnostic and research laboratories. Monitoring of DNA amplification can be done using fluorescent sequence-specific probes, which generate signal only upon binding to their target. Numerous fluorescent dyes with unique emission spectra are available and can be used to differentially label probes for various genes. Such probes can be added to the same PCR amplification reaction for simultaneous detection of multiple targets in a single assay. Such multiplexing is advantageous, since it markedly increases throughput and decreases costs and labor. Here, we describe application of multiplex real-time RT-PCR using TaqMan probes in the analysis of relative expression levels of a novel tumor-associated gene CUG2 in cell lines and tissue samples.