Impermeable soybean seeds commonly referred to as 'Ishimame' in Japan are undesirable for the soybean food industries. The trait is widely accepted as a physical dormancy and its mechanism is considered as a difference in microstructure of the seed coat, which functions as a barrier to water and gases. We have hypothesized that the topography of pores in the seedcoat plays an important role in water uptake. The topographic differences in pores between the permeable and the impermeable seeds were investigated by using a digital imaging microscope equipped with laser profi ling system. On the permeable seeds, 44. 8 pores with a 10 μm depth and width were counted in 0. 5 × 0. 7 mm of the coat surface, whereas only 3. 2 pores were found on the impermeable seed coat. To clarify the effect of the pores on the permeability, depth-controlled depressions (pores) were formed on the impermeable seed coat by using a commercial diamond whetstone. Pores with depths of ca. 20 μm were suffi cient to restore the impermeable seeds to the permeable ones. The permeable seed coat had pores that reached the palisade layer of the coat. The pores are suggested to the major pathways for the water uptake.