Methods: In this observational associated study, we analyzed CTLA-4 (rs3087243, rs231775), FOXO-3 (rs2802292, rs9400239), and PTPN-22 (rs12730735) polymorphisms in 277 adults with T1DM, assessing associations with probiotic and vitamin D use, self-reported dietary patterns, metabolic control, autoimmune thyroid disease (AITD), and metabolic dysfunction-associated steatotic liver disease (MASLD). Here, FOXO3 is linked to autoimmune thyroid disease.