The effects of fuel composition on homogeneous charge compression ignition (HCCI) combustion were studied experimentally in an engine employing negative valve overlap (NVO). Three test fuels, varying in ignition quality and volatility, were investigated for their effect on engine performance and combustion phasing; comparisons were made to a full-run 87-octane base fuel. The three test fuels, which varied in research octane number from 69 to 98, were all found to advance the combustion timing slightly relative to the base fuel, suggesting some differences in the ignition chemistry. The combustion performance at a fixed combustion phasing, however, was found to be comparable, within the limits of the system, for all of the fuels. A major testing issue that limited the system repeatability was the formation of combustion chamber deposits under some operating conditions. A methodology to mitigate these effects was employed with some success. Under no conditions did any of the test fuels exhibit two-stage, or low temperature, ignition. To further investigate this, n-heptane was tested, and it too did not show any low temperature heat release except for conditions that had very little heat release during the NVO period. Chemical kinetic simulations of the ignition delay were performed and confirmed that the high temperature, low density charge that results from NVO causes the ignition chemistry to circumvent the T-p regime where low temperature heat release occurs. High temperature heat release is less sensitive to fuel composition.