This study aimed to determine the most suitable plant cell tissue organ (PCTO) culture technique and methyl jasmonate (MeJA) concentration to produce caffeic acid derivatives (CADs) with high efficiency from Echinacea purpurea. To this aim, 50, 100, 150, and 200 mu M MeJA were applied to callus, shoot and root cultures formed from in vitro plantlets. Biomass and growth indexes were determined at the end of the culture periods. To understand the effects of MeJA on secondary metabolite (SM) accumulations and production efficiency, the amounts of CADs and total phenolic contents (TPC) produced both in the dry extract and in flasks were analysed by HPLC and spectrophotometer. Results were compared with field-grown 2-year-old E. purpurea. It was observed that biomass and growth indexes were negatively affected in all of the callus, shoot and root cultures by treatments with MeJA. However, the applications increased the accumulation of total phenolics and CADs, especially when at the concentrations of 100 and 150 mu M MeJA. The TPC of the shoots and roots that were not treated with MeJA were fourfold higher, while the CADs were eightfold higher than the calli without MeJA. Production per flask in callus, shoot and root cultures were at optimum levels with 100 mu M MeJA. As a result, MeJA increased the accumulation amount and production efficiency of total phenolics and CADs in all three PCTO culture techniques. However, with the application of 100 and 150 mu M MeJA to root cultures, the highest efficiency of total phenolic and CAD productions was achieved. When the optimum concentrations of MeJA were applied to the root cultures of E. purpurea, SMs could be produced in an amount close to the 2-year-old plants grown in the field.