This study describes a method for reducing the emissions of toxic organic pollutants from heavy duty diesel engines fueled by biodiesel produced from waste cooking oil (WCO). An analytical method was developed to simultaneously measure five pollutants from one exhaust sample, namely polycyclic aromatic hydrocarbons (PAHs), polychlorined dibenzo-p-dixins and dibenzofurans (PCDD/Fs), polychlorinated biphenyls (PCBs), polybrominated dibenzo-p-dioxins and dibenzofurans (PBDD/Fs) and polybrominated diphenyl ethers (PBDEs). As yet, no data regarding PBDD/F emissions from mobile sources has been reported in the literature. The mass concentrations in the exhaust, in order, were PAHs >> PBDEs >> PBDD/Fs > PCBs > PCDD/Fs, while for the pollutants having dioxin-like toxicity, their toxicity concentrations, in order, were PCDD/Fs > PBDD/Fs > PCBs. These concentrations were two to four orders higher than those in the atmosphere. Even though the chlorine content in the WCO-based biodiesel was five times higher than that of fossil diesel, the reduction in the emission factors of the aforesaid pollutants increased along with the percentage of biodiesel. For example, B20 achieved a 49%-73% and 61%-83% reduction in mass and toxicity, respectively. In conclusion, the use of WCO-based biodiesel not only solves the problem of waste oil disposal, but also reduces the toxic organic pollutant emissions from diesel engines.