Biodiesel derived from waste cooking oil (WCO) is gaining increased attention as an alternative fuel due to lower particulate emissions and other beneficial factors such as low cost and utilization of waste oil. However, very little information is available on toxicity of airborne particulate matter (PM) emitted from biodiesel combustion. In this study, PM emitted from WCO-derived biodiesel (B100) was analyzed for its toxic potential together with ultra low sulphur diesel (ULSD) as a reference fuel and their blend (B50). Human lung epithelial carcinoma cells (A549) were used for this comparative toxicity study. Results indicate that cytotoxicity and oxidative stress were higher for B100 relative to ULSD. Furthermore, caspase 3/7 activity indicates that cell death induced by B100 was due to either caspase independent apoptotic process or other programmed cell death pathways. The toxicity was also evaluated for different engine load conditions. It was observed that at lower loads there was no significant difference in the toxicological response of B100 and ULSD. However, with increase in the engine load, B100 and B50 showed significantly higher toxicity and oxidative stress compared to ULSD.