The most significant potentially carcinogenic substances arising from a state-of-the-art clinical waste incinerator (CWI) and vehicle emissions were identified as polychlorinated dibenzo-p-dioxins, polycyclic aromatic hydrocarbons (PAHs), benzene, 1-butadiene, arsenic, cadmium, chromium and nickel. Long-term exposures of the notional maximum exposed individual (MEI) in the local environment, together with aggregate emissions from transport of clinical waste, were estimated. Mass emission rates of PAHs from the CWI to air were compared with previously published estimates of mass emissions to land from CWI bottom ash. Aggregate emissions from road transport of clinical waste were of a similar order to stack emissions from incineration. Mass emissions of PAHs to landfill generally greatly exceeded those from stack emissions. Emissions associated with operation of the CWI present a negligible contribution to overall cancer risk from PAHs and other carcinogens. Uncertainty in the quantitative risk estimates presented here is discussed in the context of these findings.