This study aimed to investigate carbonyl emissions of a diesel engine operating with commercial diesel fuel (CDF) as reference, and 10% and 20% energy-based substitution of this, by bioethanol fumigated in the intake manifold (dual-fuel mode). Exhaust gas samples gathered in dinitrophenylhydrazine (DNPH) cartridges, were analyzed with high performance liquid chromatography (HPLC). Results showed that the addition of bioethanol reduces the acrolein and propionaldehyde compounds in exhaust emissions. On the contrary, the acetaldehyde, formaldehyde, benzaldehyde and butyraldehyde emissions increased significantly. The emission factor of total carbonyls increased 11.6 and 15 times with respect to CDF for 10% and 20% of bioethanol substitution, respectively. This work enforces the necessity of carrying out detailed evaluation of this unregulated harmful emissions for humans before promoting the partial replacement of diesel by bioethanol under dual fuel mode.