Abstract Background Health administrative data were increasingly used for chronic diseases (CDs) surveillance purposes. This cross sectional study explored the agreement between Belgian compulsory health insurance (BCHI) data and Belgian health interview survey (BHIS) data for asserting CDs. Methods Individual BHIS 2013 data were linked with BCHI data using the unique national register number. The study population included all participants of the BHIS 2013 aged 15 years and older. Linkage was possible for 93% of BHIS-participants, resulting in a study sample of 8474 individuals. For seven CDs disease status was available both through self-reported information from the BHIS and algorithms based on ATC-codes of disease-specific medication, developed on demand of the National Institute for Health and Disability Insurance (NIHDI). CD prevalence rates from both data sources were compared. Agreement was measured using sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) ...