The effect of biodiesel produced from waste cooking oil (WCO) on the particulate matters (PM) of a direct injection (DI) diesel engine was experimentally investigated and compared with commercial diesel fuel. Soot agglomerates were collected with a thermophoretic sampling device installed in the exhaust pipe of the engine. The morphology of soot particles was analyzed using high resolution transmission electron microscopy (TEM). The elemental and thermogravimetric analysis (TGA) were also conducted to study chemical composition of soot particles. Based on the TEM images, it was revealed that the soot derived from WCO biodiesel has a highly graphitic shell-core arrangement compared to diesel soot. The mean size was measured from averaging 400 primary particles for WCO biodiesel and diesel respectively. The values for WCO biodiesel indicated 19.9 nm which was smaller than diesel’s 23.7 nm. From the TGA results, WCO biodiesel showed faster oxidation process. While the oxidation of soot particles from diesel continued until 660°C, WCO biodiesel soot oxidation terminated at 560°C. Elemental analysis results showed that the diesel soot was mainly composed of carbon and hydrogen. On the other hand, WCO biodiesel soot contained high amount of oxygen species.