The Federal Joint Committee (FJC; Gemeinsamer Bundesausschuss, G-BA) defines the health-care elements that are to be reimbursed by sickness funds. To define a directive, the FJC can commission benefit assessments, which provide an overview of the scientific evidence regarding the efficacy and benefits of an intervention. This paper describes the operational implementation of the legal requirements with regard to the benefit assessments of medicines. Such benefit assessments are sometimes referred to as "isolated benefit assessments," to distinguish them from benefit assessments as part of a full economic evaluation.The FJC has the freedom to commission these assessments from any agency; however, to date the majority have commissioned the Institute for Quality and Efficiency in Health Care (IQWiG). Nevertheless, the content of this paper applies integrally to any institute commissioned for such assessments. In this report, 'the institute' is used when the text refers to any of these institutes.The legal framework for benefit assessments is laid out in the German Social Code Book version V ( http://www.sozialgesetzbuch.de ), Sects. 35b ( section 1), 139a ( section 4-6) and Sect. 139b ( section 3). It is specified that: The institute must guarantee high transparency. The institute must provide appropriate participation of relevant parties for the commission-related development of assessments, and opportunity for comment on all important segments of the assessment procedure. The institute has to report on the progress and results of the work at regular intervals. The institute is held to giving the commission to external experts. Based on the legal framework, the institute must guarantee a high procedural transparency. Transparency of the whole process should be achieved, which is evidenced by clear reporting of procedures and criteria in all phases undertaken in the benefit assessment. The most important means of enhancing transparency are: 1. To implement a scoping process to support the development of the research question. 2. To separate the work of the external experts performing the evidence assessment from that of the institute formulating recommendations. Therefore, the preliminary report as produced by external experts needs to be public, and published separately from any subsequent amendments or (draft-)reports made by the institute, which includes the institute's recommendations. 3. To implement open peer review by publishing both the comments of the reviewers and their names. Based on the legal framework, the institute must provide for adequate participation of relevant parties. These include organisations representing the interests of patients; experts of medical, pharmaceutical and health economic science and practice; the professional organisations of pharmacists and pharmaceutical companies; and experts on alternative therapies. Patients and health care professionals bring in new insights with respect to research priorities, treatment and outcomes.The relevant parties should be identified and contacted whenever the global scope of the assessment has been drafted. Subsequently, the relevant parties should be involved in defining the research question, developing the protocol and commenting on the preliminary report. To implement the involvement of relevant parties in defining the research question a scoping process is suggested. For the other phases, written comments followed by an oral discussion should be used. Finally, the relevant parties should have the right to appeal the final decision on judicial grounds. None of these steps mean that the institute would lose any part of its scientific independence.From the relevant sections of the legal framework with respect to the assessment methods, it can be concluded that: 1. The institute must ensure that the assessment is made in accordance with internationally recognised standards of evidence-based medicine (EBM). 2. The assessment is conducted in comparison with other medicines and treatment forms under consideration of the additional therapeutic benefit for the patients. 3. The minimum criteria for assessing patient benefit are improvements in the state of health, shortening the duration of illness, extension of the duration of life, reduction of side effects and improvements in quality of life. EBM refers to the application of the best available evidence to answer a research question, which can inform questions about the care of patients. The optimal design, even for effectiveness questions, is not always the randomised, controlled trial (RCT) but depends on the research question and the outcomes of interest. To increase transparency for each question, the levels of evidence examined should be made explicit. There is no empirical evidence to support the use of cutoff points with respect to the number of studies before making recommendations. To get the best available evidence for the research question(s), all relevant evidence should be considered for each question, and the best available evidence should be used to answer the question. Separate levels of evidence may have to be used for each outcome.There are many ways in which bias can be introduced in systematic reviews. Some types of bias can be prevented, other types can only be reported and, for some, the influence of the bias can be investigated. Reviews must show that potential sources of bias have been dealt with adequately.Methods used by other agencies that perform benefit assessments are useful to interpret the term 'international standards' to which the institute must comply. The National Institute for Health and Clinical Excellence (NICE) is a good example in this respect. NICE shows that it is possible to have transparent procedures for benefit assessments but that this requires detailed documentation. NICE has implemented an open procedure with respect to the comments of reviewers, which makes the procedure transparent. Although the Institute for Quality and Efficiency in Health Care (IQWiG) in Germany invites comments on their protocol and preliminary report by posting them on their website, and comments are made public, the individual comments are not evaluated openly, and therefore it remains uncertain whether or not they lead to changes in the reports. The participation of relevant parties in the assessment process as implemented by NICE guarantees a process that is transparent to all relevant parties.Transparency of the whole process is assured by clear reporting of procedures and criteria in all phases undertaken in the benefit assessment. In a scoping process, a draft scope is commented on first in writing and subsequently in the form of a scoping workshop. In this way, all relevant aspects can be heard and included in the final scope. The protocol is then developed, followed by evidence assessment. The methods used should be completely reported to show readers that the assessment has been performed with scientific rigour and that bias has been prevented where possible. All relevant parties should have the opportunity to comment on the draft protocol and the draft preliminary report. Each comment should be evaluated as to whether or not it will lead to changes, and both the comments and the evaluation should be made public to ensure transparency of this process. The same procedure should be used for the peer-review phase. Based on the final report of the evidence assessment, the institute forms recommendations and the FJC appraises the evidence.During the writing of the final report, a separation between the evidence assessment and the evidence-appraisal phase should be implemented. Ideally, this separation should be legally enforced to prevent any confusion about conflict of interests.Such a process guarantees a feasible combination of the legal requirements for transparency and involvement of relevant parties with international standards of EBM to ensure that the benefit assessments of medicines in Germany are performed according to the highest standards.