Improving oxygen reduction in microbial fuel cell (MFC) cathodes requires a better understanding of the effects of the catalyst binder chemistry and properties on performance. A series of polystyrene-b-poly(ethylene oxide) (PS-b-PEO) polymers with systematically varying hydrophilicity were designed to determine the effect of the hydrophilic character of the binder on cathode performance. Increasing the hydrophilicity of the PS-b-PEO binders enhanced the electrochemical response of the cathode and MFC power density by ∼15%, compared to the hydrophobic PS-OH binder. Increased cathode performance was likely a result of greater water uptake by the hydrophilic binder, which would increase the accessible surface area for oxygen reduction. Based on these results and due to the high cost of PS-b-PEO, the performance of an inexpensive hydrophilic neutral polymer, poly(bisphenol A-co-epichlorohydrin) (BAEH), was examined in MFCs and compared to a hydrophilic sulfonated binder (Nafion). MFCs with BAEH-based cathodes with two different Pt loadings initially (after 2 cycles) had lower MFC performance (1360 and 630 mW m-2 for 0.5 and 0.05 mg Pt cm-2) than Nafion cathodes (1980 and 1080 mW m -2 for 0.5 and 0.05 mg Pt cm-2). However, after long-term operation (22 cycles, 40 days), power production of each cell was similar (∼1200 and 700-800 mW m-2 for 0.5 and 0.05 mg Pt cm-2) likely due to cathode biofouling that could not be completely reversed through physical cleaning. While binder chemistry could improve initial electrochemical cathode performance, binder materials had less impact on overall long-term MFC performance. This observation suggests that long-term operation of MFCs will require better methods to avoid cathode biofouling. © 2011 The Royal Society of Chemistry.