BACKGROUND: Prevalence estimates of chronic medical conditions and their multiples (multimorbidity) in the general population are scarce and often rather speculative in Switzerland. Using complementary data sources, we assessed estimates validity of population-based prevalence rates of four common chronic medical conditions with high impact on cardiovascular health (diabetes mellitus, hypertension, dyslipidemia, obesity). METHODS: We restricted our analyses to patients 15-94 years old living in the German speaking part of Switzerland. Data sources were: Swiss Health Survey (SHS, 2007, n = 13,580); Family Medicine ICPC Research using Electronic Medical Record Database (FIRE, 2010-12, n = 99,441); and hospital discharge statistics (MEDSTAT, 2009-10, n = 883,936). We defined chronic medical conditions based on use of drugs, diagnoses, and measurements. RESULTS: After a careful harmonization of the definitions, a high degree of concordance, especially regarding the age- and gender-specific distribution patterns, was found for diabetes mellitus (defined as drug use or diagnosis in SHS, drug use or diagnosis or blood glucose measurement in FIRE, and ICD-10 codes E10-14 as secondary diagnosis in MEDSTAT) and for hypertension (defined as drug use alone in SHS and FIRE, and ICD-10 codes I10-15 or I67.4 as secondary diagnosis in MEDSTAT). A lesser degree of concordance was found for dyslipidemia (defined as drug use alone in SHS and FIRE, and ICD-10 code E78 in MEDSTAT), and for obesity (defined as BMI ≥ 30 kg/m2 derived from self-reported height and weight in SHS, from measured height and weight or diagnosis of obesity in FIRE, and ICD-10 code E66 as secondary diagnosis in MEDSTAT). MEDSTAT performed well for clearly defined diagnoses (diabetes, hypertension), but underrepresented systematically more symptomatic conditions (dyslipidemia, obesity). CONCLUSION: Complementary data sources can provide different prevalence estimates of chronic medical conditions in the general population. However, common age and sex patterns indicate that a careful harmonization of the definition of each chronic medical condition permits a high degree of concordance.