The hindered diffusion and binding of proteins of different sizes (lysozyme, BSA and IgG) in an agarose gel is described using adsorption kinetic and diffusional data together with an experimentally determined pore size distribution in the gel. The validity of the pore model, including variable diffusion coefficients and porosities is tested against experimental confocal microscopy data. No fitting parameters were used in the present model. The importance of knowing the gel structure is demonstrated especially for large proteins such as IgG. Experimental confocal microscopy data can be explained by the present model.