Background: Selective IgA deficiency (SIgAD) is the most common primary immunodeficiency disorder, which is characterized by significantly decreased serum levels of IgA. Abnormalities of CD4+CD25highforkhead box P3 (FoxP3)+ regulatory T cells (Treg) have been shown in association with autoimmune and inflammatory disorders. Methods: In order to evaluate the relationship between autoimmunity and Treg in SIgAD, we studied 26 IgA-deficient patients (aged 4–17 years) with serum IgA levels <7 mg/dl, 26 age- and sex-matched healthy controls and 26 age- and sex matched idiopathic thrombocytopenic purpura cases with normal immune system. Treg were determined by flow cytometry using Treg markers, including CD4, CD25 and FoxP3. Results: The mean percentage of CD4, CD25+FoxP3+ Treg from all CD4+ cells was 4.08 ± 0.86 in healthy controls, which was significantly higher than in SIgAD patients (2.93 ± 1.3; p = 0.003). We set a cutoff point (2.36%) for Treg, which was two standard deviations lower than the mean of normal controls. According to this cutoff point and in order to assess the role of Treg in clinical SIgAD manifestation, we classified patients into two groups: 16 patients in G1 with Treg <2.36% and 10 patients in G2 with Treg >2.36%. Autoimmunity was recorded in 9 patients (53.3%) of G1 and only 1 patient of G2, respectively (p = 0.034). Although a defect in class switching recombination was observed in 40% of the patients in G1, none of the G2 patients had such a defect (p = 0.028). Conclusion: This study showed decreased proportions of Treg in SIgAD patients, particularly in those with signs of chronic inflammation.