Background: A priority area in the field of substance dependence treatment is reducing the rates of relapse. Previous research has demonstrated that telephone delivered continuing care interventions are both clinically and cost effective when delivered as a component of outpatient treatment. This protocol describes a NSW Health funded study that assesses the effectiveness of delivering a telephone delivered continuing care intervention for people leaving residential substance treatment in Australia. Methods/design: All participants will be attending residential alcohol and other drug treatment provided by The Salvation Army or We Help Ourselves. The study will be conducted as a randomised controlled trial, where participants will be randomised to one of three treatment arms. The treatment arms will be: (i) 12-session continuing care telephone intervention; (ii) 4-session continuing care telephone intervention, or (iii) continuing care plan only. Baseline assessment batteries and development of the participants' continuing care plan will be completed prior to participants being randomised to a treatment condition. Research staff blind to the treatment condition will complete follow-up assessments with participants at 3-months and 6-months after they have been discharged from their residential service. Discussion: This study will provide comprehensive data on the effect of delivering the continuing care intervention for people exiting residential alcohol and other drug treatment. If shown to be effective, this intervention can be disseminated to improve the rates of relapse among people leaving residential alcohol and other drug treatment.