Concern with climate change and energy security has generated interest in both cogeneration and biofuels. This experimental study examines the performance of a residential microcogeneration system based on a Stirling engine fueled by diesel and biodiesel. Run on diesel, the system achieves a power efficiency of 11.7% and a heat efficiency of 78.7%. The corresponding efficiencies for the system, when run on biodiesel, are slightly lower at 11.5% and 77.5%, respectively. Particulate emissions for biodiesel are 69.2 mg/kWh, an order of magnitude higher than that of diesel (2.3 mg/kWh). The total unburned hydrocarbon emissions for biodiesel are higher than those of diesel. Emissions of carbon monoxide, nitrogen dioxide, methane, acetylene, ethylene, formaldehyde, and acetaldehyde are comparable between diesel and biodiesel, but nitric oxide emissions for diesel are observed to be higher at 151 ppm compared to those for biodiesel (117 ppm). The difference in the performance of the system is generally attributed to higher boiling range compounds in biodiesel that affect the flame stability, the fuel evaporation, and the complete burnout of the fuel. The system achieves energy efficiencies comparable to those of internal-combustion-engine-based and fuel-cell-based cogeneration systems.