Substance misuse in those with severe mental health problems is common and associated with poor engagement in treatment and treatment outcomes. Up to 44% of those admitted into psychiatric inpatient facilities have coexisting substance-misuse problems. However, this is not routinely addressed as part of their treatment plan. A mental health admission may present a window of opportunity for inpatients to reevaluate the impact of their substance use. This study will aim to evaluate the effectiveness of a targeted brief motivational intervention in improving engagement in treatment and to assess how feasible and acceptable this intervention is to inpatients and staff as a routine intervention.Methods/design: This randomized controlled trial will use concealed randomization; blind, independent assessment of outcome at 3 months; characterization of refusers and dropouts; and be analyzed according to the intention-to-treat principle. After baseline assessments, eligible participants will be randomized either to the Brief Integrated Motivational Intervention plus Treatment As Usual, or Treatment as Usual alone. Eligible participants will be those who are new admissions; >18 years; ICD-10 diagnosis of -schizophrenia or related disorder, bipolar affective disorder, recurrent depressive disorder, and DSM-IV diagnosis of substance abuse or dependence over the last 3 months. The primary outcome is engagement in treatment for substance misuse, and secondary outcomes include readiness to change substance misuse together with a cost-effectiveness analysis. Qualitative interviews with staff and participants will assess the acceptability of the intervention.