Pancreas beta-cell autoantibodies are important tools in prediction of type 1 diabetes, however, background frequencies of these markers reveal considerable population-specific variations. The aim of current study was to determine the frequency of glutamic acid decarboxylase (65kD) antibodies (GADA) in healthy Hungarian schoolchildren (n = 2,664) and to correlate development of GADA with HLA DQ genotypes. GADA was determined using a radioligand assay (cut-off limit: 97.5th percentile); HLA DQ genotypes were identified with allele-specific polymerase chain reaction. Thirty-five children (1.3%) tested positive for GADA among which the proportion of girls was significantly higher when compared with boys (1.8% and 0.8%, p = 0.03). The study population was followed for 5.2 years and one girl in the whole cohort, who tested positive for GADA, has developed diabetes. HLA DQ2/DQ8 and DQ2/y genotypes (where y not equal DQB1*0302, *0301, *0602, *0603) were significantly more prevalent in the GADA positive group than in antibody negative children (17.1% vs 1.7%, p = 0.0003 and 25.7% vs 10.3%, p = 0.027, respectively). In conclusion, the prevalence of GADA in the Hungarian general population is in the middle of the range found in other Caucasian ethnic groups. Individuals carrying HLA DR3-DQ2 haplotype and females were more prone to develop GADA. We suggest that for future screening programs it is important to determine predictive value of islet-cell antibodies in populations with varying disease incidence.