Cell suspension cultures of Saussurea medusa were grown in shake flasks and a 5-l stirred tank bioreactor. Biomass and jaceosidin distribution in cell aggregates of different sizes were investigated during the cultivation period. The results showed that on day 10, jaceosidin accumulation showed an increase with increasing size of the cell aggregate to 4 mm in diameter, with the highest jaceosidin accumulation being 12.2 mg/g. An inverse tendency was observed with cell aggregates larger than 4 mm in diameter, with the lowest accumulation being 3.1 mg/g. However, all of the cell aggregates, despite their size, synthesized almost the same amount of jaceosidin at day 12. Oxygen diffusion limitation and cell-cell contact may explain this behavior. In comparison with cells cultivated in shake flasks, decreased biomass and decreased jaceosidin concentration were observed when the cells were cultivated in a stirred tank bioreactor. The sublytic effects caused by the hydrodynamic stress in combination with insufficient nutrients in the bioreactor may cause cell damage.