: Main causes of death in Greece are cardiovascular diseases (CVDs), malignant neoplasms, respiratory diseases, and road traffic crashes. To assess the population health status, monitor health systems, and adjust policies, national population-based health surveys are recommended. The previous health surveys that were conducted in Greece were restricted to specific regions or high-risk groups. : This paper presents the design and methods of the Greek Health Examination Survey EMENO (National Survey of Morbidity and Risk Factors). The primary objectives are to describe morbidity (focusing on CVD, respiratory diseases, and diabetes), related risk factors, as well as health care and preventive measures utility patterns in a random sample of adults living in Greece. : The sample was selected by applying multistage stratified random sampling on 2011 Census. Trained interviewers and physicians made home visits. Standardized questionnaires were administered; physical examination, anthropometric and blood pressure measurements, and spirometry were performed. Blood samples were collected for lipid profile, glucose, glycated hemoglobin, and transaminases measurements. The survey was conducted from May 2013 until June 2016. : In total, 6006 individuals were recruited (response rate 72%). Of these, 4827 participated in at least one physical examination, 4446 had blood tests, and 3622 spirometry, whereas 3580 provided consent for using stored samples for future research (3528 including DNA studies). Statistical analysis has started, and first results are expected to be submitted for publication by the end of 2018. : EMENO comprises a unique health data resource and a bio-resource in a Mediterranean population. Its results will provide valid estimates of morbidity and risk factors’ prevalence (overall and in specific subdomains) and health care and preventive measures usage in Greece, necessary for an evidence-based strategy planning of health policies and preventive activities. [JMIR Res Protoc 2019;8(2):e10997]