The effect of pre-treatment on the permeation property of the Nafi on ionomer membrane has been evaluated. The membranes were subjected to diff erent pre-treatment procedures, viz treated with acid at room temperature, boiling with acid or boiling with water followed by cold acid. Different characterization techniques were used to understand the changes. From UV-Visible spectra, it was possible to identify the presence of water clusters and this was found to be maximum when the membrane was boiled with acid. Thermal analysis of the membranes also reflected the changes in structure due to pre-treatment. The characterizations of dye loaded membranes were also carried out. Image analysis refl ected the changes in structure due to pre-treatment. The spectrophotometric and thermal studies of the dye loaded membranes carried out showed that the two dyes interacted diff erently with Nafion. The permeation of dyes through Nafi on showed that values of permeability and diffusion coefficients were also dependent on the nature of both the dye and pre-treatment procedure.