The ethics of health incentive research—a form of public health research—are not well developed, and concerns of justice have been least examined. In this paper, we explore what potential long term harms in relation to justice may occur as a result of such research and whether they should be considered as part of its ethical evaluation. ‘Long term harms’ are defined as harms that contribute to existing systematic patterns of disadvantage for groups. Their effects are experienced on a long term basis, persisting even once an incentive research project ends. We will first establish that three categories of such harms potentially arise as a result of health incentive interventions. We then argue that the risk of these harms also constitutes a morally relevant consideration for health incentive research and suggest who may be responsible for assessing and mitigating these risks. We propose that responsibility should be assigned on the basis of who initiates health incentive research projects. Finally, we briefly describe possible strategies to prevent or mitigate the risk of long term harms to members of disadvantaged groups, which can be employed during the design, conduct and dissemination of research projects.