The purpose of this research is to investigate the impact of fuel composition on auto-ignition in homogeneous charge compression ignition (HCCI) engines in order to develop a future metric for predicting fuel performance in future HCCI engine technology. A single-cylinder, variable compression ratio engine operating as an HCCI engine was used to test reference fuels and gasoline blends with octane numbers (ON) ranging from 60 to 88. Correlations between fuel composition, ON, and two existing methods for predicting fuel auto-ignition in HCCI engines (Kalghatgi's octane index and Shibata and Urushihara's HCCI index) are investigated. Results show that octane index and HCCI index poorly predict the impact of fuel composition on auto-ignition for fuels with the same ON. The effect of ethanol in delaying auto-ignition depends on the composition of the original gasoline blend; the same is true for the addition of naphthenes. Low-temperature heat release (LTHR) correlates well with auto-ignition for gasoline fuels exhibiting LTHR.