In order to investigate HLA-DRB1 and HLADQB1 gene polymorphisms in Northern Greek pediatric population with Hashimoto's thyroiditis (HT), we analyzed the distribution of these alleles in 17 patients and in 181 healthy subjects using polymerase chain reaction. No significant association was detected between HT and alleles analyzed. However, HLA-DQB1*05 was significantly increased in patients with age of diagnosis > 10 years (87.5%) compared to those with age of diagnosis <or= 10 years (33.3%) (P=0.05). These results question the role of sexual maturity in combination with HLA-DQB1*05 as predisposing factor for the onset of HT in Northern Greek children and adolescents.