Detection of disseminated tumor cells in the blood circulation is important in assessing tumor progression. The objective of this examination was to develop a highly specific and sensitive quantitative realtime reverse transcriptase-polymerase chain reaction (qRT-PCR) assay for the detection of relevant tumor-associated transcripts in patients' blood. The qRT-PCR assays detect the human epidermal growth factor receptor 2 (HER2) and CK20 transcripts of two tumor cells spiked into 5 mL of blood after an immunomagnetic tumor cell enrichment. Furthermore, the HER2 assay is only specific when enrichment is included. This procedure is a useful alternative to fluorescence in situ hybridization and immunocytochemistry for gene alteration analysis in human tumors. The analysis of the studied molecular markers of tumor cells in blood may be useful in the detection of disseminated tumor cells as well as for monitoring treatment response, early detection of relapse, and for stratification of patients with carcinoma.