BACKGROUND:People with serious mental illness (SMI) die many years prematurely, with rates of premature mortality two to three times greater than the general population. Most premature deaths are due to "natural causes," especially cardiovascular disease and cancer. Often, people with SMI are not well engaged in primary care treatment and do not receive high-value preventative and medical services. There have been numerous efforts to improve this care, and few controlled trials, with inconsistent results. While people with SMI often do poorly with usual primary care arrangements, research suggests that integrated care and medical care management may improve treatment and outcomes, and reduce treatment costs. METHODS:This hybrid implementation-effectiveness study is a prospective, cluster controlled trial of a medical home, the SMI Patient-Aligned Care Team (SMI PACT), to improve the healthcare of patients with SMI enrolled with the Veterans Health Administration. The SMI PACT team includes proactive medical nurse care management, and integrated mental health treatment through regular psychiatry consultation and a collaborative care model. Patients are recruited to receive primary care through SMI PACT based on having a serious mental illness that is manageable with treatment, and elevated risk for hospitalization or death. In a site-level prospective controlled trial, this project studies the effect, relative to usual care, of SMI PACT on provision of appropriate preventive and medical treatments, health-related quality of life, satisfaction with care, and medical and mental health treatment utilization and costs. Research includes mixed-methods formative evaluation of usual care and SMI PACT implementation to strengthen the intervention and assess barriers and facilitators. Investigators examine relationships among organizational context, intervention factors, and patient and clinician outcomes, and identify patient factors related to successful patient outcomes. DISCUSSION:This will be one of the first controlled trials of the implementation and effectiveness of a patient centered medical home for people with serious mental illness. It will provide information regarding the value of this strategy, and processes and tools for implementing this model in community healthcare settings. TRIAL REGISTRATION:ClinicalTrials.gov, NCT01668355 . Registered August 20, 2012.