The effect of impeller clearance on flow structure and mixing time was simulated using a commercial software package CFX 4.3 and was measured experimentally. The mixing time calculated by simulation exhibited good agreement with the experimental data. The trend of forming independent flow compartments by each impeller became stronger as the clearance between two impellers increased. The homogeneity in the bioreactor was affected mainly by flow exchange between the compartments by each impeller. The most efficient mixing occurred when the impeller clearance was in the range of 0.2-0.4 vessel diameter.