Background: The death of a child before or shortly after birth is frequently preceded by an end-of-life decision (ELD). Population-based studies of incidence and characteristics of ELDs in neonates and infants are rare, and those in the foetal-infantile period (> 22 weeks of gestation - 1 year) including both neonates and stillborns, are nonexistent However, important information is missed when decisions made before birth are overlooked. Our study protocol addresses this knowledge gap. Methods: First, a new and encompassing framework was constructed to conceptualise ELDs in the foetal-infantile period. Next, a population mortality follow-back survey in Flanders (Belgium) was set up with physicians who certified all death certificates of stillbirths from 22 weeks of gestation onwards, and infants under the age of a year. Two largely similar questionnaires (stillbirths and neonates) were developed, pilot tested and validated, both including questions on ELDs and their preceding decision-making processes. Each death requires a postal questionnaire to be sent to the certifying physician. Anonymity of the child, parents and physician is ensured by a rigorous mailing procedure involving a lawyer as intermediary between death certificate authorities, physicians and researchers. Approval by medical societies, ethics and privacy commissions has been obtained. Discussion: This research protocol is the first to study ELDs over the entire foetal-infantile period on a population level. Based on representative samples of deaths and stillbirths and applying a trustworthy anonymity procedure, the research protocol can be used in other countries, irrespective of legal frameworks around perinatal end-of-life decision-making.