Several studies have shown that downregulation of GALNT2 (Polypeptide N‐Acetylgalactosaminyltransferase 2), encoding polypeptide N‐acetylgalactosaminyltransferase 2, decreases high‐density lipoprotein cholesterol (HDL‐C) and increases triglycerides levels by glycosylating key enzymes of lipid metabolism, such as angiopoietin like 3, apolipoprotein C‐III, and phospholipid transfer protein. GALNT2 is also a positive modulator of insulin signaling and action, associated with in vivo insulin sensitivity and during adipogenesis strongly upregulates adiponectin. Thus, the hypothesis that GALNT2 affects HDL‐C and triglycerides levels also through insulin sensitivity and/or circulating adiponectin, is tested. In 881 normoglycemic individuals the G allele of rs4846914 SNP at the GALNT2 locus, known to associate with GALNT2 downregulation, is associated with low HDL‐C and high values of triglycerides, triglycerides/HDL‐C ratio, and theHomeostatic Model Assessment of insulin resistance HOMAIR (p‐values = 0.01, 0.027, 0.002, and 0.016, respectively). Conversely, no association is observed with serum adiponectin levels (p = 0.091). Importantly, HOMAIR significantly mediates a proportion of the genetic association with HDL‐C (21%, 95% CI: 7–35%, p = 0.004) and triglyceride levels (32%, 95% CI: 4–59%, p = 0.023). The results are compatible with the hypothesis that, besides the effect on key lipid metabolism enzymes, GALNT2 alters HDL‐C and triglyceride levels also indirectly through a positive effect on insulin sensitivity.