AIRE expression in thymus is downregulated by estrogen after puberty, what probably renders women more susceptible to autoimmune disorders. Here we investigated the efects of minipuberty on male and female infant human thymic tissue in order to verify if this initial transient increase in sex hormones - along the frst six months of life - could afect thymic transcriptional network regulation and AIRE expression. Gene co-expression network analysis for diferentially expressed genes and miRNA-target analysis revealed sex diferences in thymic tissue during minipuberty, but such diferences were not detected in the thymic tissue of infants aged 7–18 months, i.e. the non-puberty group. AIRE expression was essentially the same in both sexes in minipuberty and in non-puberty groups, as assessed by genomic and immunohistochemical assays. However, AIRE-interactors networks showed several diferences in all groups regarding gene-gene expression correlation. Therefore, minipuberty and genomic mechanisms interact in shaping thymic sexual dimorphism along the frst six months of life.