Summary Objectives To describe the strengths and weaknesses of two Mexican health care providers for poor populations [Ministry of Health (MoH) and Social Security (SS)] in order to facilitate policy decisions about the future of the two systems. Methodology In four Mexican states we conducted (i) a household interview survey in 10 724 households; (ii) a user satisfaction survey in 1319 households; (iii) a satisfaction survey of 236 health workers; (iv) in-depth interviews with 190 health workers; (v) 188 focus-group discussions with different population groups; (vi) a document analysis. Results Both systems serve populations with similar characteristics of poverty. The availability of resources was better in the MoH system; SS care was better concerning process indicators (family planning, antenatal care; in-service delivery of drugs, staff productivity, user satisfaction and staff motivation), efficiency and effectiveness (reduction of morbidity and mortality). Possible explanatory factors for the better performance of the SS system were strong supervision, regular communication, joint data analysis and annual population surveys. Conclusion Better service organization makes a difference regarding efficiency and effectiveness. Policy-makers, deciding on which kind of health services are best for the poor, should take into account health services’ analyses.