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The effect of five different storage conditions on the total phenolic content (TPC), the antioxidant capacity (AC), the phenolic compound profile, the total amount of quantified phenolics, the hexanal content, and the sensory characteristics of hazelnuts of two cultivars (Tonda Gentile Trilobata or TGT and Delisava—harvest 2010 and 2011) were investigated for two consecutive years. The storage variables were time (0, 4, 8 and 12 months), temperature (ambient temperature, refrigeration at 5 °C, or frozen at −25 °C) and O 2 availability (ambient air, vacuum or modified atmosphere). Comparing the cultivars, Delisava exhibited the highest levels of TCP and AC for both harvests and all storage conditions; however, it was characterized by the highest hexanal content (more than sixfold higher than TGT). At the end of the storage, the TPC and AC decreased with respect to day 0 in both cultivars, with AC losses ranging between 12% and 35% and TPC losses of approximately 15%. However, these parameters were not able to distinguish the storage conditions. The hazelnut phenolic compound profiles did not seem to be affected by storage techniques in either cultivar; additionally, the sensory analysis panellists were not able to discriminate between the storage conditions. Hexanal was confirmed to be a good marker of lipid oxidation, and its content generally increased during storage in both cultivars; nevertheless, changes were well-controlled by storage conditions where low temperature and reduced oxygen worked synergistically. The absence of oxygen seemed to be more relevant with respect to low temperature, and a good preservation of raw hazelnut kernels was achieved by storage under vacuum with or without preliminary nitrogen flushing. [ABSTRACT FROM AUTHOR]