Detection of circulating tumor cells (CTC) in peripheral blood has been investigated for its prognostic ability, and its potential to measure the effectiveness of treatment(s) in patients with melanoma. However, a highly sensitive and specific assay is required to detect CTC in patients’ blood. We have developed a multimarker quantitative real-time reverse transcriptase polymerase chain reaction (RT-qPCR) assay for detecting CTC directly from peripheral blood specimens without the need of separating CTC from leukocytes (PBL). We selected and optimized four mRNA biomarkers (MART-1/Melan-A, MAGE-A3, PAX3, and GalNAc-T) for detection and prediction of clinical outcome in melanoma patients. Our protocol has both high sensitivity and specificity for CTC in blood specimens—detecting approximately one to five melanoma cells in 107 PBL. We have demonstrated the significance of this assay for serial bleed assessment of CTC in clinical trials and for daily clinical usage.