Premixed or partially premixed compression ignition modes, such as homogeneous charge compression ignition (HCCI), have been a particular focus among researchers because of their potential to deliver enhanced fuel efficiency and meet exhaust emissions mandates without the addition of costly after-treatment technologies as currently required with traditional spark ignition (SI) and direct injection compression ignition (DICI) engines. These advanced combustion strategies thus seek to combine the advantages of SI and DICI engines while avoiding their disadvantages. Previous studies have suggested that future fuels with desired properties for optimal performance in these advanced combustion modes might have properties between that of traditional gasoline and diesel fuels and will most likely consist of mixtures of petroleum derived products (aromatics, straight and branched alkanes), alcohols, synthetic alkanes, and fatty acid methyl esters. Existing ignition quality metrics such as Octane or Cetane Number are reasonably consistent for petroleum-derived fuels in SI and CI engines but can fail to adequately characterize autoignition in advanced combustion modes, particularly when higher concentrations of alcohols are included in the blend. Accordingly, in this study, the autoignition behavior of primary reference fuels (PRF) and blends of n-heptane/n-butanol were examined in a Waukesha Fuel Ignition Tester (FIT) and a Homogeneous Charge Compression Engine (HCCI). Fourteen different blends of iso-octane, n-heptane, and n-butanol were tested in the FIT ' 28 test runs with 25 ignition measurements for each test run, totaling 350 individual tests were done in all. These experimental results supported previous findings that fuel blends with similar octane numbers can exhibit very different ignition delay periods. The present experiments further showed that n-butanol blends behaved unlike PRF blends when comparing the autoignition behavior as a function of the percentage of low reactivity component. These same fuel blends were also tested in a John Deere 4024T diesel engine, which was modified to operate in HCCI mode. The HCCI and FIT experimental results were compared against multi-zone models with detailed chemical kinetic mechanisms for PRF's and n-butanol. For both the FIT and HCCI engine data, a new n-butanol/n-heptane kinetic model is developed that exhibits good agreement with the experimental data. The results also suggest that that the FIT instrument is a valuable tool for analysis of high pressure, low temperature chemistry and autoignition for future fuels in advanced combustion engines.