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Five diesel samples were analyzed by gas chromatography-mass spectrometry (GC-MS) using six GC temperature programs, aiming to investigate the effect of temperature program on association and discrimination of the samples. Temperature programs varied by ramp rate and incorporated one- or two-step temperature ramps. Pearson product moment correlation coefficients and principal components analysis were used to evaluate differences in discrimination among the diesel samples afforded by each temperature program, based on the total ion chromatogram (TIC) and selected extracted ion profiles (EIPs). Association of diesel replicates and discrimination among samples based on the TIC and aromatic EIP were similar for all temperature programs based on scores plots. The alkane EIP was not useful in discriminating samples regardless of temperature program, because of similar alkane content of the diesel samples. The association and discrimination of diesel samples was largely unaffected by temperature programs that incorporated one- or two-step temperature ramps.