The highest annual increase in the incidence of type 1 diabetes (T1D) in children under the age of 5 years and aggressive process of β-cell destruction in this age group indicate the need to assess the immune system. The aim of this study was to evaluate regulatory T cells (Tregs) frequency in the peripheral blood of children <5 years of age with newly diagnosed T1D in comparison with diabetic children diagnosed at a later age and healthy controls. 40 children with newly diagnosed T1D (20 children <5 years of age and 20 older patients) and 40 age-matched controls were included in this study. Flow cytometric analysis of Tregs was performed using the following markers: CD4, CD25, CD127, FoxP3, IL-10, and TGF-β. Apoptosis was measured using anti-active caspase 3 monoclonal antibody. Fasting C-peptide and HbA1c were monitored as well. We showed that T1D children <5 years had lower C-peptide concentration than diabetic children ≥5 years of age (0.32 vs. 0.80 ng/ml, respectively, p = 0.0005). There was lower frequency of CD4(+)CD25(high)CD127(low)FoxP3(+) Tregs in T1D children <5 years than ≥5 years of age (0.87 vs. 1.56 %, respectively, p = 0.017). Diabetic children <5 years had lower CD4(+)CD25(high)CD127(low)FoxP3(+), CD4(+)CD25(high)IL-10, and CD4(+)CD25(high)TGF-β Tregs compared to age-matched controls. There was no difference in Tregs apoptosis between the examined groups. This study highlights the distinctiveness of diabetes in children <5 years of age. Understanding the differences of immune system activity in the young diabetic children would open the way to identify children at risk for T1D and enables the use of novel forms of intervention.