AbstractIntroductionPopulation‐level changes in microcephaly incidence risk (IR) could signal circulation of neurotropic pathogens or potential emerging teratogen exposure.MethodsIn this retrospective population cohort study, we estimated the IR of hospitalizations with a microcephaly ICD‐9‐CM discharge diagnosis code among infants ≤1 year over a 15‐year period (1999–2013) using the Electronic Health Record (EHR) database from all hospital discharges in California from the Office of Statewide Hospital Planning and Development (OSHPD) database. We calculated the overall and yearly IRs per 10,000 live births (LBs) and per 10,000 hospitalizations in infants ≤1 year, and explored the impact in the IR estimates when children with microcephaly associated comorbidities were excluded or not.ResultsAmong 8,860,153 hospital discharges of infants ≤1 year in the OSHPD database over this 15 year period, we identified 6,004 hospitalizations with a microcephaly discharge diagnosis code; 3,526 of those were in neonates ≤30 days. The IR of microcephaly hospitalizations for infants ≤1 year was 7.70/10,000 LB (for neonates it was 4.52/10,000 LB) and 6.78 per 10,000 hospitalizations ≤1 year. There was large heterogeneity in the yearly microcephaly IRs (I2 = 66.6%).DiscussionEHR collected data could be used as a complementary approach to track epidemiologic changes in microcephaly IRs. However, standardization in the use of microcephaly discharge diagnosis code and harmonization in the types of additional comorbidities to be excluded across analyses is mandatory to allow for prompt identification of true changes in microcephaly rates over time.