Abstract Background In 2018 the first Belgian Health Examination Survey (BELHES) took place. The target group included all Belgian residents aged 18 years and older. The BELHES was organized as a second stage of the sixth Belgian Health Interview Survey (BHIS). This paper describes the study design, recruitment method and the methodological choices that were made in the BELHES. Methods After a pilot period during the first quarter of the BHIS fieldwork, eligible BHIS participants were invited to participate in the BELHES until a predefined number ( n = 1100) was reached. To obtain the required sample size, 4918 eligible BHIS participants had to be contacted. Data were collected at the participant’s home by trained nurses. The data collection included: 1) a short set of questions through a face-to-face interview, 2) a clinical examination consisting of the measurement of height, weight, waist circumference, blood pressure and for people aged 50 years and older handgrip strength and 3) a collection of blood and urine samples. The BELHES followed as much as possible the guidelines provided in the framework of the European Health Examination Survey (EHES) initiative. Finally 1184 individuals participated in the BELHES, resulting in a participation rate of 24.1%. Results for all the core BELHES measurements were obtained for more than 90% of the participants. Conclusion It is feasible to organize a health examination survey as a second stage of the BHIS. The first successfully organized BELHES provides useful information to support Belgian health decision-makers and health professionals. As the BELHES followed EHES recommendations to a large extent, the results can be compared with those from similar surveys in other EU (European Union) member states.