Reproducibility of performances of microbial fuel cells (MFC) started up in sulfur-containing wastewaters was examined. Four identical dual-chambered MFCs cultivated with identical inoculum, feed, cell geometry and cultivation protocol yielded distinct cell performances. Imposing positive or negative potential on anode did not enhance the performance reproducibility. Two anodes in the same anodic compartment could behave very differently. Both biofilms and anodic suspensions held specific substances with redox activities that may relate to the electron transport process. The electrolyte resistance in anodic compartment was found to principally determine the MFC power output. This study noted that the MFC performance depends heavily on biofilm, cell geometry (including anode position) and internal hydrodynamic environment.