Most of the technical know-how and experience of bioreactor engineering is applicable to plant cell cultures. In this study, transgenic rice cell cultures using RAmy3D promoter were used for the production of human cytotoxic T-lymphocyte antigen 4-immunoglobulin (hCTLA4Ig). In process aspect, the rice cells during production phase are strongly influenced by hydrodynamic stresses, such as shear stress and bubble burst. Therefore, the effects of agitation and aeration rates on cell growth and hCTLA4Ig production were investigated in a 3-L multi-bioreactor. By increasing over 240 rpm, the detrimental effects on cell growth and hCTLA4Ig production were observed. At an aeration rate of 0.3 vvm, relative cell viability sharply decreased 2 days earlier than those of lower aeration rates. In addition, it was confirmed that the specific yields and the specific productivity at 0.3 vvm were superior to those values at 0.05 vvm. Overall, higher aeration rate showed the improved hCTLA4Ig production in combination experiment. High aeration rates in general, however, have an undesired effect as excessive aeration was found to negatively affect the quality of hCTLA4Ig. Consequently, the hydrodynamic conditions must be tightly regulated during bioreactor operation in order to enhance hCTLA4Ig productivity and quality in transgenic rice cell cultures.