This is the second brief in a series of three on HIV phylogenetics. 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. This brief summarises the ways in which phylogenetic (and other sequence-based) analyses are currently being used and reflects on how they could be used in the future in the field of HIV research and public health. The third brief discusses the ethical challenges of using HIV phylogenetics in research and public health surveillance.