BACKGROUND: In the general population the prevalence of bipolar and schizophrenia is 0.24% and 1.4% respectively. People with schizophrenia and bipolar disorder have a significantly reduced life expectancy, increased rates of unemployment and a fear of stigma leading to reduced self-confidence. A core outcome set is a standardised collection of items that should be reported in all controlled trials within a research area. There are currently no core outcome sets available for use in effectiveness trials involving bipolar or schizophrenia service users managed in a community setting. METHODS: A three-step approach is to be used to concurrently develop two core outcome sets, one for bipolar and one for schizophrenia. First, a comprehensive list of outcomes will be compiled through qualitative research and systematic searching of trial databases. Focus groups and one-to-one interviews will be completed with service users, carers and healthcare professionals. Second, a Delphi study will be used to reduce the lists to a core set. The three-round Delphi study will ask service users to score the outcome list for relevance. In round two stakeholders will only see the results of their group, while in round three stakeholders will see the results of all stakeholder group by stakeholder group. Third, a consensus meeting with stakeholders will be used to confirm outcomes to be included in the core set. Following the development of the core set a systematic literature review of existing measures will allow recommendations for how the core outcomes should be measured and a stated preference survey will explore the strength of people's preferences and estimate weights for the outcomes that comprise the core set. DISCUSSION: A core outcome set represents the minimum measurement requirement for a research area. We aim to develop core outcome sets for use in research involving service users with schizophrenia or bipolar managed in a community setting. This will inform the wider PARTNERS2 study aims and objectives of developing an innovative primary care-based model of collaborative care for people with a diagnosis of bipolar or schizophrenia.