BACKGROUND: An estimated 2.7 million Latin Americans reside in Europe, mostly in Spain. Part of a broader project aimed at developing a research agenda on the health status and determinants of this population, this qualitative study engaged Latin American migrants in the identification of research priorities. METHODS: We conducted 30 group discussions between November 2012-March 2013 with 84 participants purposively selected for maximum diversity in Madrid and Barcelona (Spain). We facilitated sequences of task-oriented visual activities to explore their views on priority health concerns. We tape-recorded and transcribed discussions and developed a coding frame based on socio-ecological frameworks, which we applied to all the data using NVIVO-10. A final round of eight group discussions allowed us to triangulate and enrich interpretations by including participants' insights. FINDINGS: The cumulative toll of daily stresses was the major health concern perceived by a population that conceptualised ill-health as a constellation of symptoms rather than as specific diseases. Work-related factors, legislative frameworks regulating citizenship entitlements and feeling ethnically discriminated were major sources of psycho-social strain. Except for sexually transmitted infections, participants rarely referred to communicable diseases as a concern. The perception that clinicians systematically prescribed painkillers discouraged health seeking and fostered self-medication. Participants felt that the medicalised, chemicalised, sexually liberal and accelerated culture of the host society damaged their own, and the local populations' health. CONCLUSION: Health systems bear a disproportionate responsibility in addressing health problems rooted in other sectors. Occupational and migration policies should be recognised explicitly as health policies. The mismatch between researchers' emphasis on communicable infections and the health concerns of Latin American migrants highlights the need for greater interaction between different forms of knowledge. In this process, the biomedical culture of reliance on pharmacological solutions should not remain unquestioned.