Quantitative real-time polymerase chain reaction (qRT-PCR) is a useful technique to measure the changes in gene expression analysis. However, it is very important to choose the appropriate reference gene(s) for accurate comparison of mRNA transcriptes in different samples and tissues. No specific reference genes have been reported for chicory root and leaf tissues so far. We optimized a simple method for the analysis of tissue-specific gene expression in chicory root cultivar (Cichorium intybus).