Microbial fuel cells (MFCs) are devices that can use bacterial metabolism to produce an electrical current from a wide range organic substrates. Due to the promise of sustainable energy production from organic wastes, research has intensified in this field in the last few years. While holding great promise only a few marine sediment MFCs have been used practically, providing current for low power devices. To further improve MFC technology an understanding of the limitations and microbiology of these systems is required. Some researchers are uncovering that the greatest value of MFC technology may not be the production of electricity but the ability of electrode associated microbes to degrade wastes and toxic chemicals. We conclude that for further development of MFC applications, a greater focus on understanding the microbial processes in MFC systems is required.