Medical guidelines are intended to guide decisions and criteria regarding diagnosis, management, and treatment. Strategy is to review, summarize and evaluate the best evidence and most current data on prevention, diagnosis, prognosis and therapy. Then the most important questions related to clinical practice are defined and all possible decision options and their outcomes are identified. There are currently about 800 German guidelines available, classified into 3 levels. Only 50 of them are of the highest, the so-called S-3 level, incorporating expert opinion on the basis of current evidence within the paradigm of evidence-based medicine. To date, Complementary and Alternative Medicine (CAM) is not yet a well integrated part of existing medical guidelines. However, responding to patient request the medical societies react to the change in medical culture, acknowledging CAM and involving CAM experts into the guideline process. The process of developing guidelines involves the identification of key search words and the search for relevant systematic reviews (SR) and publications of randomized controlled trials (RCT) in defined databases. In most cases evaluation is performed according to the 5 grade classification (1–5) of the Oxford Centre of Evidenced Based Medicine. This classification leads to the definition of the 4 grades (A–D) of recommendation. Only SR and/or RCT with an Oxford classification grade 1 can achieve highest recommendation A. During a consensus conference, evaluations and recommendations with their corresponding evidence are discussed. Several guidelines also list the strength of consensus found for each item. It is possible to integrate and incorporate CAM into medical guidelines however study quality is generally low. There are several CAM specific difficulties investigators are facing: e.g. randomization is sometimes difficult, because patients often refuse to accept the conventional treatment in the control group, and for some procedures, like acupuncture or cupping, blinding is impossible. The paper will focus on the general procedures developing guidelines and evidence grades for recommendations and discuss the particular problems of CAM research (blinding, sham procedures) and how the impact of these specificities affects their appearance in the guideline. However, the authors are convinced based on experience in several guidelines, that CAM can be successfully incorporated.