In situ Fourier transform infrared microspectroscopy was used to study the heat stability of proteins and hydrogen bonding interactions in dry maturation-defective mutant seeds of Arabidopsis thaliana. α-Helical, turn and β-sheet conformations were the major protein secondary structures in all of these seeds. On heating, intermolecular extended β-sheet structures, typical of protein denaturation, were formed in abscisic acid-insensitive (abi3) and leafy cotyledon (lec) mutant seeds. Proteins in dry wild-type seeds did not denature up to 150°C, but those in dry desiccation-sensitive, lec1-1, lec1-3 and abi3-5 seeds did at 68, 89 and 87°C, respectively. In the desiccation-tolerant abi3-7 and abi3-1 seeds, denaturation commenced above 120 and 135°C, respectively. Seeds of the aba1-1 abi3-1 double mutant showed signs of denaturation already upon drying. The molecular packing in the seeds was studied by observing the shift in the position of the OH-stretching vibration band with temperature. The maximal rate of change of this band with temperature was much higher in the desiccation-sensitive abi3-5, aba1-1 abi3-1, lec1-1, and lec1-3 mutant seeds than in the desiccation-tolerant wild-type, abi3-1, abi3-7, and lec2-1 seeds. We interpret this to mean that the molecular packing density is higher in dry desiccation-tolerant than in dry desiccation-sensitive seeds, which is associated with a higher or lower protein denaturation temperature, respectively. The results are discussed in relation to the physiological and biochemical characteristics of these mutant seeds.