The use of fatty acid methyl esters (FAME), often referred to as biodiesel, instead of fossil diesel fuel is under consideration in order to increase the share of fuels from renewable sources and to reduce green house gas emissions. An alternative fuel must be technically feasible, economically competitive, environmentally acceptable and easily available. Fatty acid methyl esters have found to befit all these essential qualities. Fatty acid methyl esters derived from various vegetable oils / animal fats have gained importance as an alternative fuel for diesel engines and almost no modifications are required for using biodiesel. The research on alternative fuels for compression engine has become essential due to depletion of petroleum products and its major contribution for pollution, where vegetable oil promises best alternative fuel. Vegetable oils, due to their agricultural origin are able to reduce net CO2 emissions to the atmosphere. But the major disadvantage of vegetable oil is its viscosity which is higher than diesel. In this study, the Methyl Ester of Cotton Seed oil (MECSO) and Methyl Ester of Mango Seed oil (MEMSO) from non-edible oils of Cotton seed oil and Mango seed oil are prepared, their properties are compared in order to meet EN 14214/ASTM D6751 Standards for biodiesel and with the standards of diesel fuel.