We compared the methodology and the recommendations of evidence-based guidelines for the management of fibromyalgia syndrome (FMS) to give an orientation within the continuously growing number of reviews on the therapy of FMS. Systematic searches up to April 2008 of the US-American National Guideline Clearing House, the Scottish Intercollegiate Guidelines Network, the Association of the Scientific Medical Societies in Germany (AWMF) and Medline were conducted. Three evidence-based guidelines for the management of FMS published by professional organizations were identified: The American Pain Society (APS) (2005), the European League Against Rheumatism (EULAR) (2007), and the AWMF (2008). The steering committees and panels of APS and AWMF were comprised of multiple disciplines engaged in the management of FMS and included patients, whereas the task force of EULAR only consisted of physicians, predominantly rheumatologists. APS and AWMF ascribed the highest level of evidence to systematic reviews and meta-analyses, whereas EULAR credited the highest level of evidence to randomised controlled studies. Both APS and AWMF assigned the highest level of recommendation to aerobic exercise, cognitive-behavioral therapy, amitriptyline, and multicomponent treatment. In contrast, EULAR assigned the highest level of recommendation to a set of to pharmacological treatment. Although there was some consistency in the recommendations regarding pharmacological treatments among the three guidelines, the APS and AWMF guidelines assigned higher ratings to CBT and multicomponent treatments. The inconsistencies across guidelines are likely attributable to the criteria used for study inclusion, weighting systems, and composition of the panels.