We found that PDX1-rs9581943 significantly decreased the risk of T2DM among patients aged ≤ 60 years in the codominant (OR = 0.66, 95% CI = 0.45–0.98, p = 0.039) and dominant models (OR = 0.69, 95% CI = 0.48–1.00, p = 0.049). The gene discussed is PDX1; the disease is type 2 diabetes mellitus.