Real time PCR is a powerful tool for studying the expression of genes involved in the pathophysiology of human diseases. Recent studies of the RAN (6p21), ZHX-2 (8q24.3), CHC1L (13q14.3) loci highlight the importance of these genes in multiple myeloma (MM) prognosis and therapeutic applications. Here, we described a detailed Real-Time PCR method for the detection of RAN, ZHX-2, and CHC1L expression, which could be applied in clinical situations. The expression profiles of these genes were studied in peripheral blood lymphocytes of healthy individuals, patients suffering from MM, and in the myeloma cell line, MOLP-8. Low expression levels of RAN, ZHX-2, and CHC1L were observed in myeloma patients, compared with peripheral blood lymphocytes and MOLP-8 cells. An inhibitor of histone deacetylases (TSA) had the ability to decrease expression of CHC1L and ZHX-2 in MOLP-8 cells, while expression of RAN was relatively stable in peripheral blood lymphocytes, control MOLP-8, and TSA- or 5-azacytidine treated MOLP-8 cells. In myeloma patients, we observed significant decreases in the expression of selected genes, but it was patient-specific. Our experiments illustrate new methodological approaches and troubleshooting for conducting gene expression studies in clinical laboratories.