IntroductionThe recent severe acute respiratory syndrome coronavirus type 2 (SARS–CoV–2) pandemic had a devasting global impact. Many people suffered from coronavirus disease 2019 (COVID–19) and some experienced persistent symptoms interrupting their lives even further. The World Health Organization (WHO) defined the condition of these persistent symptoms as post–COVID–19 condition (PCC). The most prevalent PCC symptoms are fatigue, dyspnea, sleep disturbances, coughing, anosmia and ageusia, chest pain, and headaches. This article describes the protocol of the Basel Long COVID Cohort Study (BALCoS), which aims at fostering understanding of PCC and investigating underlying mechanisms for the development and course of the condition by focusing on participants′ health status and symptoms with repeated measures over one year.Methods and analysisBALCoS is a prospective single site cohort study. Inclusion criteria are a confirmed PCC diagnosis according to WHO or a subjective attribution of persistent symptoms to PCC, proficiency in German to follow study procedures, and at least 18 years of age. It comprises blood sample collections, standardized neurocognitive and psychometric tests, physical performance measures, and ecological momentary assessments (EMAs). Standardized tests and EMAs are administered at baseline (BL), and at 3–, 6–, and 12–months follow–up. At BL and 12–month follow–up, physical performance and neurocognitive abilities are assessed. Participants provide blood samples at BL. The study is exploratory in nature and a sample size of at least 120 participants is targeted. The study is part of a larger Horizon Europe Long COVID project combining mechanistic, clinical, and intervention studies within an interdisciplinary European research consortium.Ethics and disseminationThe Ethics Commission of Northwest and Central Switzerland approved the study (BASEC–ID: 2023–00359), which is registered at ClinicalTrial.gov (ID:NCT05781893). All participants provide written informed consent. Key results from the study will be published in peer–reviewed journals.Funding DetailsBALCoS is primarily funded by the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number 22.00094 in the context of the European Union′s Horizon Europe research and innovation program under grant agreement No. 101057553.