Background <p>The role of immune cell profiles at birth in determining the risk of celiac disease (CD) development is currently unestablished. This study aimed to determine the associations between T- and B-cell profiles at birth and pediatric CD.</p> Methods <p>This regional cohort study analyzed prospectively collected dried blood spots from 158 children with CD (median 7 years old at CD diagnosis) and two matched comparators each (<i>n</i> = 316). We quantified T-cell receptor excision circles (TRECs) and kappa-deleting recombination excision circles (KRECs) as measures of thymic and bone marrow output at birth. Moreover, we used epigenetic cell counting to estimate the percentages of lymphocyte subsets: CD3+, CD4+, CD8 + T cells, CD4 + memory T, regulatory T, B, and NK cells.</p> Results <p>No associations were found between measured immune cell markers at birth and CD development (all p values &gt; 0.26). The median number of copies was 120 for TRECs (IQR = 92–168) and 136 (IQR = 91–183) for CD patients and comparators, respectively, and for KRECs, it was 69 (IQR = 45–100) for CD patients and 66 for comparators (IQR = 44–93). Across the groups, there were similar median percentages of T cells (CD, 32.6% [IQR = 27.0–43.8%] vs. comparators, 33.9% [IQR = 26.3–45.7%]) and B cells (CD, 25.4% [IQR = 20.3–30.6%] vs. comparators, 24.7% [IQR = 19.9–30.8%]). The ratio of the lymphocyte subset estimates between CD patients and comparators approximated one; all p values were &gt; 0.26. The results were consistent across strata defined by sex, HLA type, and age at diagnosis.</p> Conclusion <p>Genetic and epigenetic markers for B cells and T cells in immune cell profiles at birth did not impact susceptibility to childhood-onset CD.</p>