This paper presents emissions modeling and testing of a four-stroke single cylinder diesel engine using pure soybean, cottonseed, and algae biodiesel fuels. A system level engine simulation tool developed by Gamma Technologies, GT-Power, has been used to perform predictive engine combustion simulations using direct-injection jet modeling technique.Various physical and thermodynamic properties of the biodiesel fuels in both liquid and vapor states are required by the GT-Power combustion simulations. However, many of these fuel properties either do not exist or are not available in published literatures. The properties of the individual fatty esters, that comprise a biofuel, determine the overall fuel properties of the biofuel. In this study, fatty acid profiles of the soybean, cottonseed, and algae methylester biodiesel fuels have been identified and used for fuel property calculations. The predicted thermo-physical properties of biodiesels were then provided as fuel property inputs in the biodiesel combustion simulations.Using the calculated biodiesel fuel properties and an assumed fuel injector sac pressure profile, engine emissions of the conventional diesel and biodiesel fuels have been predicted from combustion simulations to investigate emission impacts of the biodiesel fuels. Soybean biodiesel engine emissions, which include NO x , HC, CO and CO 2 , measured at various engine speeds and loads in actual combustion emissions tests performed in this study were also compared to those predicted by the combustion simulations.