We report the global structural alterations in histone H3 proteins induced by lysine-9 mono-, di- and trimethylation, which are part of the critical post-translational modifications for DNA damage responses, identified using synchrotron radiation circular dichroism (CD) spectroscopy. Compared with unmodified H3, mono- and dimethylation increases the number of α-helices and decreases the numbers of β-strands, while trimethylation decreases the α-helix content and increases the β-strand content. Comparison of the secondary-structure contents of these histone H3 proteins suggests that the methylation-induced structural alterations occur at residues not only close to but also distant from the methylated sites. Such global structural alterations may regulate the interactions of methylated histones with other molecules, such as histone-binding proteins in DNA damage repair processes.