We have conducted a detailed numerical analysis of HCCI engine operation at low loads to investigate the sources of HC and CO emissions and the associated combustion inefficiencies. Engine performance and emissions are evaluated as fueling is reduced from typical HCCI conditions, with an equivalence ratio f = 0.26 to very low loads (f = 0.04). Calculations are conducted using a segregated multi-zone methodology and a detailed chemical kinetic mechanism for iso-octane with 859 chemical species.The computational results agree very well with recent experimental results. Pressure traces, heat release rates, burn duration, combustion efficiency and emissions of hydrocarbon, oxygenated hydrocarbon, and carbon monoxide are generally well predicted for the whole range of equivalence ratios. The computational model also shows where the pollutants originate within the combustion chamber, thereby explaining the changes in the HC and CO emissions as a function of equivalence ratio. The results of this paper contribute to the understanding of the high emission behavior of HCCI engines at low equivalence ratios and are important for characterizing this previously little explored, yet important range of operation.