Determining when the combustion event occurs in a Homogeneous Charge Compression Ignition (HCCI) engine can prove challenging given that the combustion event is governed by temperature sensitive chemical-kinetics which results in auto-ignition of the fuel/air mixture. Auto-ignition variability can affect emissions and efficiency. Thus, measuring and controlling the combustion event is of the utmost importance. Ion sensors can be used reasonably to detect the combustion event for various fuels used in HCCI engines over a wide range of operating conditions. Experiments have been conducted to measure ion signals produced from the combustion of gasoline, ethanol, and n-heptane in a 4-cylinder HCCI engine with different equivalence ratios and intake pressures. It was found that the ion signal is reduced under several situations: with an increase in intake pressure, reducing equivalence ratio (under lean conditions), and decreasing the bias voltage source. Results from a Well-Mixed-Reactor (WMR) model suggest that gasoline produces more ions than both ethanol and n-heptane during combustion under the same operating conditions; these predictions are supported by experiments.