DEFA1/DEFA3 copy number less than 7 was correlated with higher susceptibility to HAIs (OR 3.014, 95% CI 1.609–5.648), and higher APS score and emergency source were associated with an increased risk for HAIs (APS score: OR 1.142, 95% CI 1.081–1.207; emergency source: OR 2.522, 95% CI 1.269–5.012). Here, DEFA3 is linked to autoimmune polyendocrinopathy.