Steroidal glycoalkaloids which serve the plant defense, are toxic secondary metabolites present in the plants of solanaceae family. The upper safe limit of glycoalkaloids for human consumption is 20mg/KG FW, excess of which may cause severe health disorders. Several factors like drought, high temperature, light exposure, and wounding increase tuber glycoalkaloid content. Among these, drought is an important factor which causes a rapid increase in potato glycoalkaloid content. Glycoalkaloid biosynthetic genes and their expression pattern need to be characterized to regulate the glycoalkaloid accumulation. Three key genes SGT1, SGT2 and SGT3 are demonstrated to be directly participated in the biosynthetic pathway for glycoalkaloid formation. Present study was focused on the study of expression pattern of key genes in GA pathway under drought stress in two different potato cultivars Atlantic and Haryoung which are low and high glycoalkaloid accumulating respectively. Drought stress was imposed by withholding water to the plants grown in pots and control plants kept irrigated. Expression analysis of SGT1, SGT2 and SGT3 was done from the leaf and tuber sample of three time intervals i.e 5, 10 and 20 days after imposing stress. Variation in the expression level of genes was observed in leaf and tuber where the fold increase in expression over control was higher in tuber sample compared to leaf. Expression levels also varied in leaf and tuber among two cultivars. However, expression of SGT1, SGT2 and SGT3 is significant indicating the involvement of these genes in glycoalkaloid accumulation under drought stress.