Purpose: The Danish Excellence Centre in Ophthalmic Epidemiology (DECODE-EYE) is a national research collaboration formed in order to study the real-life interaction between ocular and systemic disease based on the entire Danish population. Here, we aim to describe the study design and the methodology, which will be used. Methods: We will extract data from various healthcare registers and databases including the Danish Civil Registration System (unique personal identifier), the Danish National Patient Register (inpatient and outpatient visits), the Danish National Prescription Registry (redeemed prescription drugs), the National Health Service Register (data on health services in primary health care), the Danish Register of Cause of Death (data on cause of death), Statistics Denmark (demographic and socioeconomic data), the Danish Registry of Diabetic Retinopathy (level of diabetic retinopathy (DR) in diabetes patients) and the database of the Danish Association of the Blind (date and cause of blindness). Relevant registers will be linked by the unique personal identifier, and associations will be examined cross-sectional and/or longitudinally, in principle in 1:5 age- and gender-matched case–control cohort studies. Conclusion: Denmark has a strong tradition in register-based healthcare research, given a high number of validated national registers and databases. DECODE-EYE will provide Danish, large-scale data on associations between ocular and systemic disease. With a target population of 5.8 million individuals, twelve separate studies (Protocols A–L) have initially been designed to be studied in the upcoming years. These will provide novel data on interactions between systemic disease and relevant ophthalmological end-points like blindness, DR, glaucoma, corneal disease, retinal vascular disease, cataract and intravitreal angiostatic treatment.