Patient visits are an important opportunity for general practitioners (GPs) to discuss the risks of smoking and cessation strategies. In Australia, the guidelines on cessation published by the Royal Australian College of General Practitioners (the Guidelines) represent a key resource for GPs in this regard. The predominant message of the Guidelines is that pharmacotherapy should be recommended as first-line therapy for smokers expressing an interest in quitting. This, however, ignores established evidence about the success of unassisted quitting. Our analysis of the Guidelines identifies a number of potential conflicts of interest which may have affected the advice provided. These include extensive funding by the pharmaceutical industry of sources cited to support the recommendations, and relations between members of the Guidelines Content Advisory Group and the pharmaceutical industry. Recommendations issued by professional bodies have enormous potential impact upon public health and there is a need for the highest levels of scrutiny and transparency in their development. Information about research cited in guidelines should include funding sources, and developers should be free of obvious conflicts of interest. Smoking remains the leading preventable cause of global mortality. Concerns related to pharmaceutical industry funding of research, scientific integrity and recommendations on smoking cessation by medical advisory groups clearly have implications beyond Australia.