Most panels that develop clinical practice guidelines are poorly equipped to address resource allocation or cost issues associated with management options. This risks neglect, arbitrariness, lack of transparency, and methodological flaws in consideration of resource allocation. We provide recommendations for guideline panels to promote greater transparency and rigor. We suggest focusing on resource allocation issues for only a limited number of recommendations and provide criteria for selecting those in which economic considerations are likely to influence the direction or strength of the recommendation. Panels should involve a health economist to assist with the systematic review and critical interpretation of relevant economic analyses. They should carefully define the intended audience and may consider issuing alternative recommendations when available resources vary widely across target clinical settings. Targeting a limited number of recommendations for the consideration of resource allocation issues, and ensuring methodologically high-quality review, will best serve guideline panels, and the health-care providers and patients they hope to assist.