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Background: Cytokines are an important factor in immune regulation. IL-6 is a cytokine with various biological activity. Splice variants of IL6, by interaction with dissimilar receptors (IL6-R and gp130), activate distinct signal transduction for regulating multiple biological processes. Shirazi thyme (Zataria multiflora), in traditional medicine, is used as an anti-inflammatory agent. Objectives: In this study, the effect of Shirazi thyme hydro alcoholic extract, on the expression level of two different IL6 variants in human mesenchymal stem cells (MSCs), were studied. Methods:MSCs where cultured and treated in seven groups by two doses of 50 µgmL -1 and 100 µgmL -1 in three different times 2 hours, 16 hours, and 24 hours. RNA was extracted from harvested cells and cDNA was synthesized. IL6 mRNA level was evaluated by real-time qRT-PCR. 2 -∆∆Ct was used for IL6 gene expression fold changes and statistically analyzed by t-test. Results: Treatment with Shirazi thyme extract significantly reduced IL6 mRNA variant1 at all doses, and all the time, excepted in 50 µgmL -1 treatment after 16 hours, however, IL6 mRNA variant2 had increased level in all studied doses and times.Conclusions: Blocking IL6 signals or reducing its expression could be a theraptic approach for some inflammatory, malignant, or autoimmune diseases. Increased IL6 mRNA variant 2, also by increasing the sensitivity of cells to insulin and increasing the absorption of glucose and lipid metabolism, might be prevented adipose tissue expansion.