Trigonella persica is a valuable medicinal plant which comprises trigonelline that is secondary metabolite and important component in cosmetic and medicine. This research was conducted in order to evaluation the drought stress effect on growth parameters, root anatomical changes and trigonelline content in T. persica. Plants were grown under soil moisture corresponding to 100%, 75%, 50% and 25% field capacity for two weeks. The data showed that drought stress was significantly decreased fresh weight and dry weight of shoot and root. In addition, leaf area was declined due to drought stress. Interestingly, root length was enhanced by drought stress. Root microscopic study demonstrated that drought stress increased thickness of epidermal, endodermal, vascular bundle, central cylinder and parenchyma in T. persica. Drought stress caused a significant increment in alkaloid and trigonelline content in aerial parts and roots of T. persica. These results revealed that T. persica responded to drought stress by increasing the alkaloid and trigonelline, as well as the anatomical changes in root. Considering the importance of trigonline and alkaloids, this work may open prospects for production of the pharmaceutically valuable secondary metabolites thereby drought stress.