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As other auto-immune processes, thyroiditis is monitored after vaccinations. We aimed to estimate the baseline incidence of thyroiditis among girls, before studying papillomavirus vaccination as a potential risk factor. Observational cohort study including girls aged 9-18 years registered between 2002-2016 in the Spanish Primary Care Database for Pharmacoepidemiological Research (BIFAP). Girls were followed until a record of thyroiditis, 19 years of age, left the cohort, died, or the study ended. Anonymized records were reviewed for diag