Porous filtration membranes such as microfiltration and ultrafiltration membranes have been widely applied in various industries. Recently nanofiltration membranes have been commercialized. Characterization of the membrane pore structure, such as pore radius, pore density, pore shape, pore length, tortuosity, and so on, becomes more and more important and characterization methods must be established. Various methods to characterize the pore structure of porous membranes will be reviewed. Firstly, the microscopy observation method which is the most direct method to characterize the membrane pore structure is reviewed. Atomic force microscopy recently developed has been applied for the membrane observation. Secondly, methods based on bubble pressure and gas transport will be reviewed. This method can measure the pore size distribution of a membrane under wet conditions. The third method is thermoporometry. The temperature of liquid solidification and/or solid melting is lower in smaller pores and thus by measuring the freezing and/or melting thermo-diagram, the pore size and its distribution can be determined in wet environments. These three methods are not directly related with the solute or particle permeation performance which is the most important characteristics of separation membranes. Therefore the final method reviewed will be the characterization based on molecular transport through a membrane. Various transport models have been developed and they can be used for the characterization. The models and structural analysis by using the models will be explained.