A suspension of various microorganisms was cross-filtered and the filtration characteristics were studied. In crossflow filtration of Corynebacterium glutamicum, an ellipsoidal-shaped bacterium, the experimental permeation flux was in agreement with the calculated value based on the filtration theory, using the specific resistance measured in dead-end filtration and the amount of cake per unit filtration area. The cells deposited on the membrane in the same manner as in dead;end filtration. On the other hand, in crossflow filtration of Bacillus species, all of which are rod-shaped cells, the cells in the cake formed on the membrane were oriented toward the direction of the circulation flow. This arrangement of the cells increased the specific resistance of the cake, which made the flux lower than the calculated value, using the specific resistance measured in dead-end filtration. Furthermore, we clarified that the degree of the cell arrangement was dependent on the operational conditions in the crossflow filtration of rod-shaped cells.