The current research focus on fuel effects on low temperature reactions (LTR) in Homogeneous Charge Compression Ignition (HCCI) and Partially Premixed Combustion (PPC). LTR result in a first stage of heat release with decreasing reaction rate at increasing temperature. This makes LTR important for the onset of the main combustion. However, auto-ignition is also affected by other parameters and all fuel does not exhibit LTR. Moreover, the LTR does not only depend on fuel type but also on engine conditions. This research aims to understand how fuel composition affects LTR in each type of combustion mode and to determine the relative importance of chemical and physical fuel properties for PPC. For HCCI the chemical properties are expected to dominate over physical properties, since vaporization and mixing are completed far before start of combustion. The HCCI experiments were carried out in a Cooperative Fuel Research (CFR) engine, while the PPC experiments were carried out in a single cylinder high speed direct injected (HSPDI) diesel engine. A Gaussian profile was fitted to the data and used to determine the fraction of LTR for each type of combustion. The fuels used in this study are blends of ethanol, n-heptane, and isooctane (ERF), blends of toluene, n-heptane, and isooctane (TRF), and blends of toluene, ethanol, n-heptane and isooctane (TERF). The fractions of ethanol and toluene were varied at three levels to examine the influence on LTR for both HCCI and PPC. The results showed that increasing ethanol and toluene concentration in the ERF and TERF blends increases the LTR fraction in PPC while they decreased the LTR fraction for HCCI combustion. Ethanol had a stronger impact than toluene. Increasing isooctane and decreasing n-heptane concentration increased the LTR fraction for PPC while it decreased LTR fraction for HCCI. The lack of agreement between fuel effects in PPC and HCCI indicate that the processes behind LTR are more complex in PPC than in HCCI. It is not certain that a fuel with more pronounced chemical prerequisites for LTR will produce more LTR. The strong relation between LTR and ID for PPC indicate that the ignition quality is central for the fraction of LTR in PPC.