In humans, atopic dermatitis (AD) is believed to result from a complex interaction between genetic and environmental factors. Based on recent evidence, it has been proposed that neurotrophins play an important role in allergic inflammation. Levels of nerve growth factor (NGF) and brain-derived neurotrophic factor (BDNF) in blood have been found to be elevated and correlated positively with disease in AD patients. Therefore, we sought to evaluate the role of nucleotide variation in the NGFB and BDNF genes in relation to the pathogenesis of AD. A functional polymorphism within the BDNF gene (Val66Met) and six selected polymorphisms in the NGFB gene were examined in 361 German AD patients and 325 non-atopic controls. In this cohort, no significant association with AD was detected, refuting the hypothesis that variation in these two neurotrophin genes contributes substantially to AD.