Abstract: Objective To investigate the problems existing in the setting up and running of fever clinics in Shanghai since the occurrence of SARS and Bird Flu and to provide a helpful reference for establishing rational mode of fever clinics to deal with public health emergency such as SARS and Bird Flu.Methods A total of 136 fever clinics after 2006 were included in the study, and both qualitative and quantitative methods were used in data collection and analyses. Qualitative studies included interview with administrators, physicians working in the fever clinics, officers working in public health institutions. Quantitative surveys included: (1) The setting and running of the fever clinics. (2) The number of patients with fever. (3) Questionnaire survey was done among physicians working in fever clinics.Results Problems were found during the study included: (1) Problems existed in the setting and running of fever clinics and some were suspended because of hospital reconstruction, expansion and other reasons. (2) Fever patients were unclear about the treatment process, especially about the pre triage system. (3) There was significant unbalance in cost and effectiveness in most of the fever clinics.Conclusion The distribution of fever clinics in the city should be adjusted to make fever patient monitoring network cover all city people. Medical institutions should make the best use of the existing conditions and integrate the related resources for diagnosis and treatment of infectious diseases. Meanwhile, the diagnosis and treatment process for infectious diseases should be strictly enforced.