In this study, pepper inbred lines were grafted onto different pepper rootstock genotypes to investigate the rootstock effects on the plant performance based on the physiological and morphological response mechanisms under hydroponic conditions in a controlled climate chamber. Four selected pepper inbred lines (33H-3-1, 21H-1-2, ERU462 and ERU1227) were grafted onto six rootstock genotypes (46 KB F1, 5 MSIVH F1, Scarface, 11B14, Kuheylan and E21R10144), while ungrafted scion genotypes were used as control plants. Highly significant (p<0.001) differences were found in shoot and root fresh biomass, main stem length, number of leaves, leaf chrophyll index (SPAD) and total root length among graft combinations. Compared to ungrafted control plants, shoot fresh weight, and total leaf number was significantly higher by the graft combination of 21H-1-2/46 KB F1, while significantly longer main stem length was produced by ERU1227/11B14. The highest leaf SPAD value was recorded in the graft combination of 33H-3-1/11B14, whereas higher root fresh weight, and total root length were obtained when the same scion was grafted onto a different rootstock (33H-31/Kuheylan). Overall, the pepper rootstock genotypes 11B14 and 46 KB F1 showed a better performance in shoot and root growth and leaf development in different graft combinations as compared to ungrafted pepper plants. Shoot fresh biomass production of grafted plants significantly positive correlated with total root length (r: 0.79***), and root fresh weigth (r: 0.77***) whereas negatively correlated with stem length (r:-0.52*). All these suggest that the rootstocks with a vigorous root system play a major role in improvement of growth performance and development of grafted pepper plants.