AIMS/HYPOTHESIS: An association between increased length/height and weight gain and risk of type 1 diabetes (T1D) has been reported in children. We set out to investigate the potential contribution of T1D human leukocyte antigen (HLA) risk genotypes to this association in two countries with a contrasting disease incidence. METHODS: In Estonia and Finland, length and weight were monitored up to the age of 24 months in 688 subjects. According to their HLA genotypes, the children were divided into four groups, those with very high, high or moderate risk for T1D, as well as a neutral/control group. Relative length and weight (SDS) were assessed and compared at 3, 6, 12, 18 and 24 months using World Health Organization (WHO) growth curves. RESULTS: The mean relative length at the age of 24 months was lower in the group with the very high risk HLA genotype compared to the controls (p < 0.05). The mean relative weight differed between those two groups at the age of 12, 18 and 24 months (p < 0.05). When Estonian and Finnish cohorts were analyzed separately, the relative length showed similar but non-significant trends in both countries, while in Estonia the changes in weight at some time points still remained significant (p < 0.05). CONCLUSIONS: Children with the highest HLA-conferred risk for T1D gained less weight and length during the first 24 months of life, and this feature was more pronounced in the Estonian children.