Ion sensors have been shown to be a low-cost and robust method of measuring start of combustion (SOC) in Homogeneous Charge Compression Ignition (HCCI) engines. The combustion event in an HCCI engine is governed by temperature sensitive chemical-kinetics and is highly fuel dependent. Autoignition variability between various fuels can also affect emissions, efficiency, and overall operating range of the HCCI engine. Ion sensors (i.e. modified spark-plugs) can be used pragmatically to detect the combustion event for various fuels in HCCI engines over a wide range of operating conditions. An investigation of the ion currents produced from the combustion of gasoline, ethanol, and n-heptane in a 1.9L 4-cylinder VW TDI diesel engine (converted to run in HCCI mode) is conducted over a range of equivalence ratios, intake temperatures, and intake pressures. Gasoline, ethanol and n-heptane have diverse autoignition characteristics which affect the overall operation of the HCCI engine. Experiments show that detecting ions during combustion is a sufficient and reliable technique used in measuring SOC for various fuels in a HCCI engine. The ion currents for gasoline and ethanol are comparable, while n-heptane produces a much weaker ion current. The fact that gasoline and ethanol have comparable ion currents has huge implications in regards to the use of fuel blends consisting of 85% ethanol and 15% gasoline (E85) in HCCI engines. Additionally, the ability to measure ion currents using n-heptane fuel suggests ions may be measurable in diesel fueled HCCI engines.