The aim of this study was to investigate whether common variants in CTLA-4 (rs3087243, rs231775), FOXO-3 (rs2802292, rs9400239), and PTPN-22 (rs12730735) modify the association between environmental/nutritional factors (dietary patterns, vitamin D supplementation, probiotic use) and metabolic or autoimmune-related outcomes (metabolic control, autoimmune thyroid disease (AITD), metabolic dysfunction-associated steatotic liver disease (MASDL) in adults with T1D. Here, PTPN22 is linked to autoimmune thyroid disease.