Abstract Background Health surveys (HS) are a well-established methodology for measuring the health status of a population. The relative merit of using information based on HS versus electronic health records (EHR) to measure multimorbidity has not been established. Our study had two objectives: 1) to measure and compare the prevalence and distribution of multimorbidity in HS and EHR data, and 2) to test specific hypotheses about potential differences between HS and EHR reporting of diseases with a symptoms-based diagnosis and those requiring diagnostic testing. Methods Cross-sectional study using data from a periodic HS conducted by the Catalan government and from EHR covering 80% of the Catalan population aged 15 years and older. We determined the prevalence of 27 selected health conditions in both data sources, calculated the prevalence and distribution of multimorbidity (defined as the presence of ≥2 of the selected conditions), and determined multimorbidity patterns. We tested two hypotheses: a) health conditions requiring diagnostic tests for their diagnosis and management would be more prevalent in the EHR; and b) symptoms-based health problems would be more prevalent in the HS data. Results We analysed 15,926 HS interviews and 1,597,258 EHRs. The profile of the EHR sample was 52% women, average age 47 years (standard deviation: 18.8), and 68% having at least one of the selected health conditions, the 3 most prevalent being hypertension (20%), depression or anxiety (16%) and mental disorders (15%). Multimorbidity was higher in HS than in EHR data (60% vs. 43%, respectively, for ages 15-75+, P