P>Ataxia-telangiectasia (AT) is a complex disorder characterized by progressive neurodegeneration, immunodeficiency, hypersensitivity to DNA damaging agents and cancer predisposition. Clinical heterogeneity is observed even among the affected siblings with AT. Mutations of the ataxia-telangiectasia mutated (ATM) gene are responsible for AT. H2AX, an essential histone protein, is phosphorylated by ATM in response to double-strand breaks, and H2AX-deficient mice share some clinical and laboratory findings with AT. Therefore, we sought a possible modifier effect of H2AX gene on various clinical features in a group of patients with AT and healthy controls. We performed sequence analysis of H2AX gene in 81 patients with AT, and in 51 of them, we analysed methylation. We examined H2AX gene expression in 25 patients. We investigated 48 healthy individuals as a control group. We did not detect any mutation or sequence variation in the H2AX gene, or any altered methylation pattern in any of the patients. Although H2AX gene expression was markedly increased (2.5- to 11.8-fold) in five of 25 patients, and slightly increased (1.5- to 2.4-fold) in four patients, the correlations between H2AX gene expression and the evaluated clinical features of the patients were not significant. Other potential modifier genes that might be scrutinized in AT patients include p53, 53BP1 and TIP60, as well as the genes that effect mitochondrial function and the oxidative response.