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Two <i>Lactobacillus</i> strains have proven anti-inflammatory properties by reducing pro-inflammatory responses to antigens. This randomized double-blind placebo-controlled trial tested the hypothesis that <i>L. plantarum</i> HEAL9 and <i>L. paracasei</i> 8700:2 suppress ongoing celiac disease autoimmunity in genetically at risk children on a gluten-containing diet in a longitudinally screening study for celiac disease. Seventy-eight children with celiac disease autoimmunity participated of whom 40 received 10¹⁰ CFU/day of <i>L. plantarum</i> HEAL9 and <i>L. paracasei</i> 8700:2 (probiotic group) and 38 children maltodextrin (placebo group) for six months. Blood samples were drawn at zero, three and six months and phenotyping of peripheral blood lymphocytes and IgA and IgG autoantibodies against tissue transglutaminase (tTG) were measured. In the placebo group, na&#239;ve CD45RA+ Th cells decreased (<i>p</i> = 0.002) whereas effector and memory CD45RO+ Th cells increased (<i>p</i> = 0.003). In contrast, populations of cells expressing CD4+CD25^highCD45RO+CCR4+ increased in the placebo group (<i>p</i> = 0.001). Changes between the groups were observed for NK cells (<i>p</i> = 0.038) and NKT cells (<i>p</i> = 0.008). Median levels of IgA-tTG decreased more significantly over time in the probiotic (<i>p</i> = 0.013) than in the placebo (<i>p</i> = 0.043) group whereas the opposite was true for IgG-tTG (<i>p</i> = 0.062 respective <i>p</i> = 0.008). In conclusion, daily oral administration of <i>L. plantarum</i> HEAL9 and <i>L. paracasei</i> 8700:2 modulate the peripheral immune response in children with celiac disease autoimmunity.