Radicals generated in trehalose single crystals by X radiation at room temperature were investigated by electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR) and ENDOR-induced EPR measurements, together with periodic density functional theory calculations. In the first days after irradiation, three radical species (I1, I2 and I3) were detected, two of which (I1 and I2) dominate the EPR spectrum and could be identified as H-abstracted species centered at C3′ (I1) and C2 (I2), the latter with additional formation of a carbonyl group at C3. Annealing the sample at 40°C for 3 days or storing it in ambient conditions for three months resulted in another, more stable EPR spectrum. Two major species could be characterized in this stage (S1 and S2), only one of which was tentatively identified as an H-abstracted, C2-centered species (S1). Our findings disagree with a previous EPR study [Gräslund and Löfroth (23)] on several accounts. This work stresses the need for caution when interpreting composite EPR spectra and thermally induced spectral changes of radiation-induced species, even in these relatively simple carbohydrates. It also provides further evidence that the pathways for radiation damage critically depend on the specific conformation of a molecule and its environment, but also that carbonyl group formation is a common process in the radiation chemistry of sugars and related compounds.