The combination of genetic susceptibility and environmental factors can induce allergic sensitization and subsequent local inflammation, resulting in atopic dermatitis (AD). Sister chromatid exchange (SCE) is a sensitive method that may reflect an instability in DNA or a deficiency in DNA repair. The aim of the present study was to investigate whether patients with AD have defects in DNA repair and whether SCE frequency can be used as a genetic marker in the pathogenesis of AD. Between September 2004 and July 2005, SCE was analyzed in the peripheral blood lymphocyte chromosomes of 32 patients with AD and 28 control subjects at the Dermatology Unit of Erzurum State Hospital. This study found that the SCE frequency was significantly increased in patients with AD (P < 0.00001). The prevalence of SCE was not correlated with patient age, sex, disease duration or AD disease severity. Our results indicate that increased chromosome instability may play an important role in the etiology of AD.