Higher carbon alcohols such as n-propanol, n-butanol, and n-pentanol that can be produced from biomass can be used as alternative fuels in diesel engines. These alcohols can mix with both diesel fuel and biodiesel without any phase separation. Currently, unregulated emissions such as toxicity and total polycyclic aromatic hydrocarbon (PAH) from the use of these alcohols are not monitored. Investigating the effects of increasing the alternative fuel concentration for use in a diesel engine on PAH emissions will contribute to the protection of the environment and extend the engine’s operating life. In this study, the effects of adding 35% (by volume) n-propanol, n-butanol and n-pentanol to diesel and biodiesel on unregulated emissions in a diesel engine were compared. In the total PAH emission of biodiesel, the mixture containing n-pentanol stood out compared to other mixtures with a decrease of 39.17%. In higher alcohol-diesel mixtures, the highest reduction was observed in the n-butanol mixture as 80.98%. With respect to toxic emissions, very close values were obtained in biodiesel blends up to 94.15%, although n-butanol showed a maximum reduction of 84.33% in diesel blends. All these reductions also prevented the formation of high-cycle PAHs. The results obtained showed that the use of high carbon alcohols in a high mixing ratio contributed to the improvement of the fuel properties of biodiesel and to an increase in the alternative fuel mixing ratio with the reduction of PAH emissions from diesel fuel.