This brief, the third in a series of three, discusses the ethical issues arising from HIV phylogenetic analyses in both research and public health settings and offers guidance on how to minimise risks for analyses that generate sensitive data. The first brief, The Application of Phylogenetics to HIV—Insights into Biology and Epidemiology of HIV, explains the methods and approaches used to generate genetic and phylogenetic data and analyses. The second brief explores what we have learned from HIV phylogenetic studies and how HIV phylogenetics can and should be used to support public health programmes.