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Primary ciliary dyskinesia (PCD) is caused by pathogenetic variants in more than 55 genes. PCD is associated with early-onset chronic wet cough and rhinosinusitis, laterality defects, middle ear disease and reduced fertility. The clinical presentation is heterogeneous, and diagnosis often relies on multiple tests. The American Thoracic Society (ATS) and European Respiratory Society (ERS) have previously developed separate guidelines for diagnosis. Here, ERS and ATS members systematically reviewed the literature on diagnostic tools used in practice and developed unified evidence-based guidelines for PCD diagnosis using Grading of Recommendations, Assessment, Development and Evaluations methodology, and a transparent process of decision-making using evidence-to-decision frameworks. The Task Force panel formulated three PICO (Patients, Intervention, Comparison, Outcome) questions and three narrative questions. The accuracies of high-speed video microscopy, immunofluorescence and nasal nitric oxide were compared to a reference test of transmission electron microscopy and/or genetics. The panel gives a strong recommendation for use of high-speed video microscopy, immunofluorescence and nasal nitric oxide as adjunct tests to transmission electron microscopy and/or genetics for PCD diagnosis. However, no adjunct test is suitable as a standalone test to diagnose PCD and no single adjunct or reference test is suitable to exclude PCD. Pursuing a genetic diagnosis is encouraged owing to the implications for management. The panel emphasises that tests should meet a minimum standard and proposes that patients are evaluated at a referral centre experienced in diagnosis. The pre-test probability based on symptoms should be considered when interpreting results.