Poor oxidation stability is the central problem associated with the commercial acceptance of the biodiesel. The EU standard (EN14214) specifies a minimum value of 6 h for biodiesel induction period at 110°C, measured with Rancimat instrument. Most of the freshly prepared biodiesel generally have lower induction periods than prescribed by the standards. Anti-oxidants are therefore added to enhance the oxidation/ storage stability of biodiesel. Oxidation is an exothermic process, and the reaction heat evolved makes it possible to use thermo gravimetric analysis (TGA).In the present study, the oxidation stability of methyl esters derived from Karanja oil and Neem oil, stabilized with anti-oxidant pyrogalol (PY) was studied by DSC. Onset temperature of freshly prepared Karanja biodiesel (KOME) and Neem biodiesel (NOME) was observed to be 148 and 153°C respectively. The stability increases with increasing anti-oxidant dosage. A comparative analysis of oxidation stability of biodiesel/diesel blends was done on biodiesel derived from Karanja (Pongamia pinnata), Neem (Azadirachta indica) and Jatropha (Jatropha curcas) oil using Rancimat instrument. Jatropha biodiesel (JOME)/ diesel blends were observed to be most stable compared to KOME and NOME/ diesel blends. Further in this study, emissions and performance tests were conducted on an IDI diesel engine for diesel, B100, and biodiesel dosed with 1000 ppm of PY to experimentally evaluate adverse effects of anti-oxidants on biodiesel performance and emissions. With anti-oxidants dosed biodiesel, THC and CO were found to be slightly higher compared to diesel and B100. However the difference was not significant. Thermal efficiency and BSFC of anti-oxidants dosed biodiesel was comparable to diesel and B100.