It is now accepted that the transport sector is responsible for a large and growing share of global emissions affecting both health and climate. The quantification of these effects requires, as an essential first step, a comprehensive analysis and characterization of the contributing subsectors, i.e. road transport, shipping, aviation and rail. The shipping contribution in dock/harbour areas is of particular interest because many vessels use old engines powered with old technology giving rise to high levels of particulate emissions mainly because the fuel employed contains high levels of sulphur, up to 4.5%. Large amounts of polyaromatic hydrocarbons and varying contents of transition metals are also detected. Few studies on the physicochemical composition of direct emissions from ship fuels have been performed; none have been compared to actual contents in local harbour or port atmospheres. The transformation of these ship-related materials to toxicologically active species may be much more efficient than corresponding road emission or domestic sources because of the expected highly acidic nature of the particulates. Surface, toxic material may therefore become readily bioavailable under such conditions but such studies have not been performed hitherto. This mini-review outlines in detail the issues raised above in the context of measurements made in Cork, Ireland.