In October 2023, the European Medicines Agency (EMA) launched a tender for building a framework for the post-authorization safety monitoring and evaluation of vaccines in the European Union (EU) and the European Economic Area (EEA). The EU PE & PV and the VAC4EU network received and implemented the tender, thus developing the SAFETY-VAC study. This report corresponds to the second objective of the study, aiming to develop tailored algorithms, and estimates background incidence rates (IR) and 6- and 12-month cumulative IR in electronic health records (EHRs) of 10 autoimmune diseases selected based on their relevance and potential risk due to vaccination exposure: autoimmune hepatitis (AIH), erythema nodosum (EN), Graves’ disease (GD), Hashimoto´s thyroiditis (HT), multiple sclerosis (MS), systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), psoriatic arthritis (PSA), polyarteritis nodose (PAN), and ulcerative colitis (UC). A multi-database cohort design study was conducted from January 1st, 2017, till the last data availability for each data source, accessing data from 7 different EHR data sources from 5 EEA countries (Spain: BIFAP, SIDIAP, VID; the United Kingdom: CPRD; Italy: PEDIANET; France: SNDS; Norway: National Registries) that have proven to be able to convert data into the ConcePTION common data model (CDM). Clinical and operational definitions were developed for each flare based on the literature review and experts’ consultations. Study cohorts start with the first diagnosis of the autoimmune disease (diagnostic codes). Flares´ BIRs per 1,000 person-years (PY) were calculated. Follow-up began 30 to 90 days after cohort entry, depending on the disease, was interrupted 30 to 90 days by identification of a new flare or vaccination, and was stopped at the earliest of death, disenrollment, or last data extraction. Kaplan-Meier analyses calculated cumulative IR of first flare episodes at 6- and 12-months. The contribution of different algorithms’ components to BIRs was assessed for each data source. Additionally, this report estimates the background IR of flares of selected auto-immune diseases in the pregnant population, and stratification for age categories (0-17, 18-50, ≥60 years old) and gender is reported.