The aim of the work is to evaluate the damage to human health arising from emissions of in-operation internal combustion engines fed by biogas. The need of including also unregulated emissions like polycyclic aromatic hydrocarbons (PAHs), aldehydes and dioxins and furans is twofold: (i) to cover the lack in biogas engine emissions measurements and (ii) to complete the picture on biogas harmfulness to human health by identifying the substances with the highest impact. To this purpose, an experimental campaign is conducted on six biogas engines and one fed by natural gas all characterised by an electric power of 999 kWel. Collected data are used to perform an impact analysis on human health combining the Health Impact Assessment and the Risk Assessment. Measurements show that PAHs, aldehydes and diossin and furans are almost always below the detection limit, in both biogas and natural gas exhausts. The carcinogenic risk analysis of PAHs for the two fuels established their substantial equivalence. The analysis of equivalent toxicity of dioxins and furans reveals that biogas is, on average, 10 times more toxic than natural gas. Among regulated emissions, NOx in the biogas engines exhausts are three times higher than those of natural gas. They are the main contributors to human health damage, with approximately 90% of the total. SOx ranks second and accounts for about 6% of the total damage. Therefore, (i) the contribution to human health damage of unregulated emissions is limited compared to the damage from unregulated emissions, (ii) the damage per unit of electricity of biogas engines exhausts is about three times higher than that of natural gas and it is directly linked to NOx, (iii) obtaining a good estimation of the human health damage from both biogas and natural gas engines emissions is enough of a reason to consider NOx and SOx.