Dual fuel applications of alcohol fuels such as ethanol or butanol through port injection with direct injection of diesel can be effective in reduction of NOx. However, these dual fuel applications are usually associated with an increase in the incomplete combustion products such as hydrocarbons (HC), carbon monoxide (CO), and hydrogen (H2) emissions. An analysis of these products of incomplete combustion and the resulting combustion efficiency penalty was made in the diesel ignited alcohol combustion modes. The effect of EGR application was evaluated using ethanol and butanol as the port injected fuel, with varying alcohol fractions at the mid-load condition (10 -12 bar IMEP). The impact of varying the engine load (5 bar to 19 bar IMEP) in the diesel ignited ethanol mode on the incomplete combustion products was also studied. Emission measurements were taken and the net fuel energy loss as a result of the incomplete combustion was estimated. Hydrocarbon speciation and hydrogen concentration of the exhaust gas were performed by a Fourier Transform Infrared (FTIR) spectrometry gas analyzer system and a mass spectrometer respectively. Results suggested that the CO and smoke emissions rose monotonically with the application of EGR for all test conditions. While the H2 contribution to combustion inefficiency was largely insensitive to the alcohol fraction and insignificant (less than 1%), the contribution of CO and HC increased when more alcohol was used (up to 20 g/kWh and 3 g/kWh for ethanol-diesel respectively, up to 20 g/kWh and 2.5 g/kWh for butanol-diesel respectively). Analysis of the unburnt hydrocarbon species suggested that for ethanol dual fuel application, a majority of the combustion efficiency penalty could be attributed to the unburnt ethanol (between 30 to 40%). Whereas, when butanol was used, heavier HC species contributed to the combustion efficiency loss (between 30 to 50%).