Cancer screening programmes aim to save lives and reduce cancer burden through prevention or early detection of specific cancers. Risk stratification, where one or more elements of a screening programme are systematically tailored based on multiple individual-level risk factors, could improve the balance of screening benefits and harms and programme efficiency. In this article, we explore the resulting ethical issues and how they impact risk-stratified screening policymaking using Beauchamp and Childress's principles of medical ethics. First, in line with universal screening programme principles, we acknowledge that risk-stratified screening should be introduced only when the expected total benefits outweigh the harms, and where it has a favourable overall impact compared to alternative options. We then discuss how these are difficult to both value and quantify, and that risk models typically perform differently in sub-populations. Second, we consider whether screening is an individual right and whether it is fair to offer more or less intensive screening to some and not others based on personal characteristics. Third, we discuss the need to maintain respect for autonomy, including ensuring informed consent and considering the screening implications for those who cannot or choose not to participate in the risk assessment. In summary, from an ethical perspective, focusing on population-level effectiveness alone is insufficient when planning risk-stratified screening programmes and the range of ethical principles must be considered.