Introduction: Thyroglobulin (Tg) is an iodoglycoprotein synthesized by thyroid follicular cells and serves as a crucial precursor for thyroid hormone production. To date, our research group has conducted the only genome-wide association study (GWAS) on plasma Tg levels. Leveraging recent advancements in computational methods and modelling, we employed a Bayesian approach to probabilistically infer the genetic architecture of Tg. Numerous observational studies have suggested a link between thyroid function and metabolic syndrome (MetS), as well as with serum 25- hydroxyvitamin D [25(OH)D] levels, but the direction of these effects and the precise causal mechanisms remain unclear. Building on the expertise in statistical genetics acquired from our GWAS study, we subsequently applied Mendelian randomization (MR) to further explore the causal relationships between thyroid function, MetS, and serum 25(OH)D concentrations. Methods: In our initial study, we performed a GWAS of plasma Tg levels using a Bayesian sparse linear mixed model (BSLMM) and a frequentist linear mixed model (LMM) to analyze 7,289,083 genetic variants in 1,096 healthy European-ancestry participants from the Croatian Biobank. This was followed by a meta-analysis with two independent cohorts (total n=2,109) to identify genome-wide significant variants associated with Tg levels. In the first MR analysis, we utilized summary statistics from the most comprehensive GWAS available for thyroid-stimulating hormone (TSH), free thyroxine (fT4), MetS, and its components. In the second MR study, we included additional thyroid function indicators such as free triiodothyronine (fT3), total triiodothyronine (TT3), thyroid peroxidase antibody levels (TPOAb), TPOAb positivity, low TSH, high TSH, autoimmune hypothyroidism and autoimmune hyperthyroidism, as well as 25(OH)D levels. We employed the multiplicative random-effects inverse variance weighted (IVW) method for primary analysis, supplemented by weighted mode, weighted median, MR-Egger, MR-PRESSO, and CAUSE methods to ensure robust results. Results: Our meta-analysis of the GWAS data identified 83 genome-wide significant variants within the ST6GAL1 gene (p < 5 × 10-8 ) that were associated with plasma Tg levels. The SNP-heritability of Tg was estimated to be 17%, with 52% of this variation attributed to a small number of 16 variants with major effects on Tg levels. MR analyses revealed that higher fT4 levels were causally linked to a lower risk of developing MetS (OR = 0.96, p = 0.037). Additionally, fT4 was positively associated with high-density lipoprotein cholesterol (HDL-C) (β = 0.02, p = 0.008), while TSH was positively associated with triglycerides (TG) (β = 0.01, p = 0.044). Reverse MR analysis indicated that HDL-C was negatively associated with TSH (β = −0.03, p = 0.046), suggesting a bidirectional relationship between thyroid function and lipid profile. Furthermore, our MR analyses demonstrated a causal effect of serum 25(OH)D levels on high TSH, with each 1 SD increase in 25(OH)D being associated with a 12% decrease in the risk of high TSH (p = 0.02). Moreover, a 1 SD increase in serum 25(OH)D was linked to a 16.34% reduction in the risk of developing autoimmune hypothyroidism (p = 0.02). Conclusion: Our GWAS on Tg levels identified key genetic variants and provided valuable insights into the genetic architecture of Tg. We also demonstrated causal associations between variations in thyroid function and the risk of MetS, as well as the impact of vitamin D levels on thyroid function. Integrating these insights into clinical practice could enhance personalized medicine approaches, paving the way for more targeted therapeutic and preventive strategies in managing thyroid-related disorders and associated metabolic conditions.