The influence of soy- and palm-based biofuels on the in-cylinder sources of unburned hydrocarbons (UHC) and carbon monoxide (CO) was investigated in an optically accessible research engine operating in a partially premixed, low-temperature combustion regime. The biofuels were blended with an emissions certification grade diesel fuel and the soy-based biofuel was also tested neat. Cylinder pressure and emissions of UHC, CO, soot, and NOx were obtained to characterize global fuel effects on combustion and emissions. Planar laser-induced fluorescence was used to capture the spatial distribution of fuel and partial oxidation products within the clearance and bowl volumes of the combustion chamber. In addition, late-cycle (30° and 50° aTDC) semi-quantitative CO distributions were measured above the piston within the clearance volume using a deep-UV LIF technique.Compared with neat diesel fuel, the palm-based biofuel blends produced the largest decrease in UHC (38-56%) and CO (28-44%), but generated significant increases in both NOx (17-37%) and soot (41-43%). With soy-based blends, however, UHC decreased by 30-43% and CO by 17-22%, while NOx (-1-2% increase) and soot (0.8-8.5% increase) emissions varied slightly. The UHC and CO emissions were found to correlate well with the combustion phasing of each fuel at a given injection timing. The UHC PLIF measurements demonstrated several differences in the evolution of the UHC distributions throughout the cylinder volume during the mixture formation, premixed heat-release, and mixing-controlled heat-release portions of the engine cycle. However, the late-cycle UHC PLIF and spectrally resolved CO LIF measurements showed no significant differences in the main sources of UHC and CO when fueling the engine with either diesel fuel or biofuel blends.