BACKGROUND: Family law reforms in Australia require separated parents in dispute to attempt mandatory family dispute resolution (FDR) in community-based family services before court attendance. However, there are concerns about such services when clients present with a history of high conflict and family violence. This study protocol describes a longitudinal study of couples presenting for family mediation services. The study aims to describe the profile of family mediation clients, including type of family violence, and determine the impact of violence profiles on FDR processes and outcomes, such as the type and durability of shared parenting arrangements and clients' satisfaction with mediated agreements. METHODS: A mixed method, naturalistic longitudinal design is used. The sampling frame is clients presenting at nine family mediation centres across metropolitan, outer suburban, and regional/rural sites in Victoria, Australia. Data are collected at pre-test, completion of mediation, and six months later. Self-administered surveys are administered at the three time points, and a telephone interview at the final post-test. The key study variable is family violence. Key outcome measures are changes in the type and level of acrimony and violent behaviours, the relationship between violence and mediated agreements, the durability of agreements over six months, and client satisfaction with mediation. DISCUSSION: Family violence is a major risk to the physical and mental health of women and children. This study will inform debates about the role of family violence and how to manage it in the family mediation context. It will also inform decision-making about mediation practices by better understanding how mediation impacts on parenting agreements, and the implications for children, especially in the context of family violence.