375 children were tested for AIE 2011–17 (median age 11.1 years; 54% girls); 18 children (5%) were AIE antibody positive (proportion of positive tests): CSF GAD65-IgG (3.1%), plasma NMDAR-IgG (2.8%), CSF NMDAR-IgG (1.8%), plasma GAD65-IgG (1.0%), and plasma CASPR2-IgG (0.4%). Five children fulfilled the criteria for probably/definite anti-NMDAR encephalitis (incidence: 0.07/100,000 person-years; 95% CI=0.03–0.17), and 4 children with anti-GAD65 antibodies fulfilled the criteria for anti-GAD65 associated AIE (incidence=0.055/100,000 person-years, 95% CI=0.021–0.15). The incidence of “antibody negative but probable AIE” was 0.055/100,000 person-years (95% CI=0.021–0.15). The positive predictive value of ICD diagnostic codes for anti-NMDAR encephalitis was poor.