With reference to the Q fever outbreak in the Netherlands in 2009-10, we tested if an evidence-based approach, comparable to the methodology used in clinical medicine, was appropriate for giving public health advice under time constrains. According to the principles of evidence-based methodologies, articles were retrieved from bibliographic databases and categorised by type and size, outcome, strengths and limitations. The risk assessment was conducted in two months and involved six staff members. We retrieved and read 559 abstracts and selected approximately 150 full text articles. The most striking finding was the lack of sound scientific evidence behind standard treatment regimes for Q fever in pregnancy. Difficulties in applying existing evidence rating systems and in expressing uncertainties were identified as problems during the process. By systematically assessing the evidence on several questions about Q fever, we were able to draw new conclusions and specify earlier statements. We found it difficult to grade the mostly observational studies with the known evidence-based grading systems. There is need to develop new methods for grading evidence from different sources in the field of public health. We conclude that an evidence-based approach is feasible for providing a risk assessment within two to three months.