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Background: In Quebec, the influenza A (H1N1) pandemic was managed using a top-down style that left many involved players with critical views and frustrations. We aimed to describe physicians' perceptions--infectious diseases specialists/medical microbiologists (IDMM) and public health/preventive medicine specialists (PHPMS)--in regards to issues encountered with the pandemics management at the physician level and highlight suggested improvements for future healthcare emergencies., Methods: In April 2010, Quebec IDMM and PHPMS physicians were invited to anonymously complete a web-based learning needs assessment. The survey included both open-ended and multiple-choice questions. Descriptive statistics were used to report on the frequency distribution of multiple choice responses whereas thematic content analysis was used to analyse qualitative data generated from the survey and help understand respondents' experience and perceptions with the pandemics., Results: Of the 102 respondents, 85.3% reported difficulties or frustrations in their practice during the pandemic. The thematic analysis revealed two core themes describing the problems experienced in the pandemic management: coordination and resource-related difficulties. Coordination issues included communication, clinical practice guidelines, decision-making, roles and responsibilities, epidemiological investigation, and public health expert advisory committees. Resources issues included laboratory resources, patient management, and vaccination process., Conclusion: Together, the quantitative and qualitative data suggest a need for improved coordination, a better definition of roles and responsibilities, increased use of information technologies, merged communications, and transparency in the decisional process. Increased flexibility and less contradiction in clinical practice guidelines from different sources and increased laboratory/clinical capacity were felt critical to the proper management of infectious disease emergencies.