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A single cylinder engine was operated in HCCI mode with diesel-range fuels, spanning a range in cetane number (CN) from 34 to 62. In addition to measurements of standard gaseous emissions (CO, HC, and NOx), multiple sampling and analysis techniques were used to identify and measure the individual exhaust HC species including an array of oxygenated compounds. A new analytical method, using liquid chromatography (LC) with electrospray ionization-mass spectrometry (ESI-MS) in tandem with ultraviolet (UV) detection, was developed to analyze the longer chain aldehydes as well as carboxylic acids. Results showed an abundance of formic and butyric acid formation at or near the same concentration levels as formaldehyde and other aldehydes.