The European Society of Endodontology (ESE) is in the process of developing S3‐Level Clinical Practice Guidelines for the treatment of pulpal and apical disease for the benefit of clinicians and patients. In order to ensure a homogenous review process in the development of the clinical practice guidelines, it is essential that the core outcomes for all endodontic treatments are standardised and recommendations are made regarding minimum follow up time specific to each outcome measure. In the absence of a recognised core outcome set in Endodontics, the current project aimed to follow an established consensus process to define the most appropriate clinician and patient‐reported outcomes. As part of the project, recommendations will also be agreed regarding an acceptable minimum follow‐up period for studies by literature review and group discussion. The selected outcome measures and follow‐up periods will be used in subsequent systematic analyses of the literature to investigate the effectiveness of endodontic treatment to alleviate pulpitis and apical periodontitis. In this paper; previous reviews, ESE Guidelines and Position Statements were searched in order to compile a list of potentially important outcome measures for the treatment of pulpitis (working group 1), the non‐surgical treatment of apical periodontitis (working group 2), the surgical treatment of apical periodontitis (working group 3) and the regenerative treatment of apical periodontitis (working group 4). Initially, the two S3 guideline leads selected two independent senior academics with experience of evidence‐based dentistry to lead each of the four working groups forming a 10‐member steering group. The working group leads in turn selected 32 academics with experience of evidence‐based dentistry to lead the individual systematic reviews contained within the respective working groups. These 42 individuals make up the Guideline Development Group (GDG). Prior to the selected systematic reviewers commencing writing and submitting the review protocol, the complete list of outcome variables identified in this document will be ranked by the 42 members of the GDG in their importance to the individual patient using a 9‐point Likert scale. A summary of the survey scores will thereafter be shared with the members of the group and the final list of clinician and patient‐reported outcome measures rated as critical for decision making (7‐9 on Likert scale by majority of survey participants) to guide systematic reviews will be consented and confirmed during an online meeting of the steering group. In this online meeting another aspect with regard to meaningfulness of clinical trial results to be addressed in systematic reviews will be consented: length of follow‐up. In order to develop high quality guidelines, it is suggested that the follow‐up period after treatment should be related to the specific outcome measure being addressed; however, a minimum of one year for assessing the effectiveness of treatments for pulpitis and apical periodontitis should be considered. It is accepted, that selected research questions that focus on pain, swelling, medication taken or investigating diagnostic accuracy are likely to have shorter follow‐up periods. As a result of the GDG consensus process the outcome measures and length of follow‐up will, alongside the use of standard instruments to assess the methodological quality of clinical trials and other comparative studies, be applied to all the commissioned systematic reviews that will inform the subsequent process when developing the ESE S3 Level Clinical Practice Guidelines.