Subjects with celiac disease (CD) had a lower incidence of type 2 diabetes (DM2) compared to healthy controls. A gluten-free diet (GFD) did not significantly alter gut microbiota composition in patients with CD, but changes were observed between healthy individuals and CD patients without GFD. Bifidobacterium, Clostridium histolyticum, and Faecalibacterium prausnitzii were less abundant in CD patients not on a GFD compared to the control group. Lactobacillus was lower in children with active CD compared to healthy individuals and those on a GFD. Maintaining a balanced gluten-free diet is important for both newly diagnosed and ongoing celiac patients.