The main obstacle for a wider use of membrane bioreactors (MBRs) for wastewater treatment is membrane fouling, which increases operating costs. Fora more efficient control of membrane fouling in MBRs, an understanding of the mechanisms of membrane fouling is important. We conducted two separate pilot-scale experiments using real municipal wastewater to investigate the influence of the membrane flux in MBRs on the characteristics of foulants, which were analyzed by Fourier transform infrared (FTIR) spectra, C-13 nuclear magnetic resonance (NMR) spectra, monosaccharide composition and amino acid analyses. In each experiment, two identical membrane modules were submerged in the same MBR tank and were operated under different membrane fluxes. The results obtained in this study indicated that the membrane filtration flux significantly influenced membrane fouling in MBRs. Membrane fouling in the module operated with the higher flux was much greater than that of the other on the basis of the volume of filtered mixed liquor suspension. Analyses of the foulants desorbed from the fouled membranes revealed that the nature of the foulants significantly differed depending on the membrane flux despite the fact that the two modules filtered the same mixed liquor suspension at the same time. The difference in characteristics of the foulants caused by the difference in the membrane flux was similar in the two separate experiments, indicating that reproducibility of the data was sufficient. It was thought that different fractions of the mixed liquor suspension were transported to the surfaces of the membranes depending on the membrane flux and subsequently caused membrane fouling to different extents. The foulant desorbed from the membrane operated with a higher flux seemed to cause severer fouling than the foulant desorbed from the other membrane.