This study addresses the practical, methodological and ethical challenges that were found in three studies that used focus groups with people with severe mental illness, in the context of community mental health services in Brazil. Focus groups are a powerful tool in health research that need to be better discussed in research with people with severe mental illness, in the context of community mental health facilities. This study is based on the authors' experience of conducting and analyzing focus groups in three different cities - Campinas, Rio de Janeiro and Salvador - between 2006-2010. The implementation of focus groups with people with severe mental illness is discussed in the following categories; planning, group design, sampling, recruitment, group interview guides, and conduction. The importance of connecting mental healthcare providers as part of the research context is emphasized. Ethical issues and challenges are highlighted, as well as the establishment of a sensitive and empathic group atmosphere, wherein mutual respect can facilitate interpersonal relations and enable people diagnosed with severe mental illness to make sense of the experience. We emphasize the relevance of the interaction between clinical and research teams in order to create collaborative work, achieve inquiry aims, and elicit narratives of mental health users and professionals.