The effect of porosity and void distribution on permeability was investigated, using the DSMC method. The purpose of using this method was to reduce the empirical value as much as possible. Rarefied gas flow through porous media was considered in the simulation. Since there was no difference in permeability upon varying the inlet and the outlet pressure, the adequacy of the method to calculate permeability was confirmed. It was found that the average permeability increases rapidly as porosity increases in a range of porosity greater than 0.4. Furthermore, it was verified that permeability strongly depends not only on the porosity but also on the void distribution. Hence, it was clarified that it is not effective to set a certain regularity in the arrangement for modeling porous media, and that the void in the model should be distributed irregularly.