The transesterification process of vegetable oils to give biodiesel fuel is usually made with excess alcohol. When the process is completed, the reaction mixture consists of fatty acid esters, glycerol, and the remaining amount of alcohol that has not been consumed in the reaction. The mixture of those three components usually splits into two phases. The lighter phase contains the major portion of the produced biodiesel in addition to a small portion of the process byproduct, which is glycerol. The heavier phase, on the other hand, contains the major portion of glycerol and a minor amount of biodiesel. It is quite preferable that the conditions of the transesterification process are adjusted as to reduce the amount of biodiesel wasted in the lower layer as well as the amount of glycerol wasted in the upper layer In this article the conditions of the transesterification process of Jatropha oil are studied for their effect on the losses of biodiesel and glycerol as well as their effect on the chemical composition of biodiesel. These variables include the volumetric ratio of alcohol to oil as well as the alcohol type. The results of this study have shown that the transesterification of Jatropha oil using methanol rather than ethanol and the use of alcohol in less excess reduce the overall costs of wasted product and byproduct. The use of less excess alcohol is also favored to produce biodiesel containing less percentage of polyunsaturated esters. This reduces the possibility of formation of sticky polymeric deposits in the engine. These deposits may cause several problems in the engine upon long-term running.