Abstract Background Administrative and health surveys are used in monitoring key health indicators in a population. This study investigated the agreement between self-reported disease status from the Belgian Health Interview Survey (BHIS) and pharmaceutical insurance claims extracted from the Belgian Compulsory Health Insurance (BCHI) in ascertaining the prevalence of diabetes, hypertension, and hypercholesterolemia. Methods Linkage was made between the BHIS 2018 and the BCHI 2018, from which chronic condition was ascertained using the Anatomical Therapeutic Chemical (ATC) classification and defined daily dose. The data sources were compared using estimates of disease prevalence and various measures of agreement and validity. Multivariable logistic regression was performed for each chronic condition to identify the factors associated to the agreement between the two data sources. Results The prevalence estimates computed from the BCHI and the self-reported disease definition in BHIS, respectively, are 5.8% and 5.9% diabetes cases, 24.6% and 17.6% hypertension cases, and 16.2% and 18.1% of hypercholesterolemia cases. The overall agreement and kappa coefficient between the BCHI and the self-reported disease status is highest for diabetes and is equivalent to 97.6% and 0.80, respectively. The disagreement between the two data sources in ascertaining diabetes is associated with multimorbidity and older age categories. Conclusion This study demonstrated the capability of pharmacy billing data in ascertaining and monitoring diabetes in the Belgian population. More studies are needed to assess the applicability of pharmacy claims in ascertaining other chronic conditions and to evaluate the performance of other administrative data such as hospital records containing diagnostic codes.