The thermal analysis has been employed to yield information on the biodiesel ignition quality since the ignition quality influences the combustion and exhaust emissions of the fuels in a compression ignition (CI) engine. The chemical compositions of -10 petrodiesel (-10PD), soybean-based biodiesel (SME) and cottonseed-based biodiesel (CME) are analyzed by gas chromatography-mass spectrometry (GC-MS). Ignition temperature of -10PD, SME and CME is determined by thermogravimetry-differential scanning calorimetry (TG-DSC). The study shows that the biodiesel is mainly composed of fatty acid methyl esters: C14:0–C24:0, C16:1–C22:1, C18:2 and C18:3. Biodiesel ignition quality is better than petrodiesel. The ignition temperature of CME and SME is 207.4 and 213.9 °C respectively. The ignition quality of biodiesel is better with shorter carbon chain lengths and more saturated fatty acid methyl ester (SFAME).