Peppermint (Mentha piperita L., Lamiaceae) is one of the most important medicinal and aromatic plants. Menthol is the major monoterpene constituent of peppermint’s essential oil, which is used for pharmaceuticals, cosmetics and food industries. This work was aimed to study the expression pattern of important genes (Pr, Mfs, Ls) in menthol biosynthesis pathway in different plant’s organs (leaf, flower and stem) at the beginning of flowering stage. The peppermint plants were supplied from Iranian Institute of Medicinal Plants and were transferred into a greenhouse in pots. Analysis of variance showed that there is a significant difference between leaf, flower and stem, with respect to mRNA transcript level. The results of this study indicated that the level of gene expression of Pr, Mfs and Ls were altered in the different organs. There are direct relationship between the content of menthone and menthofuran and level of gene expressions of Pr and Mfs genes in flower and leaf respectively. It can be concluded that probably the expression of Mfs and Pr genes in these organs may be regulated at transcriptional level.