There has been an increasing concern about the emissions of airborne particulate matter (PM) from diesel engines because of their close association with adverse health and environmental impacts. Among the alternative fuels being considered, biodiesel made by the transesterification of waste cooking oil has received wide attention in recent years because of its low cost and the added advantage of reducing waste oil disposal. This study was conducted to make a comparative evaluation of the particulate-bound elements emitted from ultra low sulphur diesel (ULSD) and waste cooking oil-derived biodiesel (B100) and a blend of both the fuels (B50). It was observed that the PM mass concentrations were reduced by about 36% when B100 was used. Crustal elements such as Mg, K and Al were found to be in higher concentrations compared to other elements emitted from both B100 and ULSD. Zn, Cr, Cu, Fe, Ni, Mg, Ba, K were found to be higher in the biodiesel exhaust while Co, Pb, Mn, Cd, Sr, and As were found to be higher in the ULSD exhaust. To evaluate the potential health risk due to inhalation of PM emitted from diesel engines running on ULSD and B100, health risk estimates based on exposure and dose–response assessments of particulate-bound elements were calculated assuming exposure for 24 h. The findings indicate that the exposure to PM of the B100 exhaust is relatively more hazardous and may pose adverse health effects compared to ULSD.