Protein fouling is a critical problem for ultrafiltration (UF) and microfiltration (MF). In the latest decade, a Fourier-transform infrared (FT-IR) spectroscopic method has been developed to quantify protein secondary structure by employing the amide I spectral region. The most attractive feature of FT-IR analysis is its ability to analyze proteins in various conditions. In this study, we employed FT-IR to quantify the conformational change of protein fouled on polysulfone (PS) UF membrane and polytetrafluoroethylene (PTFE) MF membrane. Bovine serum albumin (BSA) was adopted as a model protein. BSA adsorption onto the membranes was performed at 4 degreesC and gel-like BSA deposits on the membranes were prepared by filtration at room temperature. FT-IR analysis revealed that the BSA adsorbed onto PS UF membrane had little change in the secondary structure, whereas the BSA adsorbed onto PTFE MF membrane had remarkable changes in the secondary structure, which were a decrease in alpha -helix content from 66 to 50% and an increase in beta -sheet content from 21 to 36%. In addition, gel-like BSA deposits on both of the membranes had marked changes in secondary structure, which were similar to the changes in the BSA adsorbed onto the PTFE MF membrane. And the BSA concentration did not significantly affect the changes in the secondary structure of BSA fouled on both the UF and MF membranes.