Background Genetic factors have an important role in atopic dermatitis (AD) predisposition. Toll like receptor (TLR) are important mediators between environment and immune system. There are incosnsitent studies about TLSR polymorphisms in AD. Objective This study examined whether single nucleotide polimorphisms (SNPs) in the genes for TLR2 and TLR4 could be associated with the AD phenotypes and with its clinical severity in a large group of Italian children. Methods 187 children with Ad and 150 healthy children were recruited. AD severity was assessed by SCORAD. TLR2 (A-16934T and R753Q polymorphisms) and TLR4 (D299G and T399I SNPs) were genotyped by PCR-RFLP. Results The frequency of the R753Q was significantly higher in AD children (16.0%) compared with controls (6.0%, P=0.004; OR2.99,95%CI 1.39–6.41; RR 1.46,95%CI 1.14–1.69). AD patients a significantly different frequency of the D299G SNP (14.9%) in comparison with the controls (6.6%, P = 0.01; OR 2.46, 95%CI 1.17–5.17; RR 2.24; 95%CI 1.15–4.45). Conclusion Children with AD may have a distinct genotype and the TLR-2 R753Q SNP was prevalent in a subset of patients with AD characterized by a more severe clinical picture.