The overall goal of this work was to stimulate and inform an evidence-based reform of mental health care in central and eastern Europe. A mix of quantitative and qualitative methods was used to analyse changes in mental health care provision during last 25 years; to deterministically link registries of mental health inpatient discharges and causes of death and assess standardized mortality ratio and causes of deaths; to explore the nature of stigma-related burden. We linked data of 283,618 individuals and demonstrated up to three-times higher mortality compared to the general population in the Czech Republic. Further, we demonstrated the pervasive nature of mental health-related stigma and discrimination in the country. Key recommendations for policy- and decision makers were formulated and communicated to the leading group of the Czech mental health-care reforms and through a WHO regional meeting and report on “Culture and reform of mental health care in CEE”.