<b><i>Background:</i></b> Cytopathology is integral to the investigation and diagnosis of respiratory disease, and, in the last decade or so, transbronchial needle aspiration by endobronchial ultrasound has made possible diagnosis and staging of malignant thoracic tumours at a single procedure. In addition, interventional teams increasingly include cytopathologists and cytotechnologists who, by providing rapid onsite evaluation, ensure efficient sampling of intrathoracic targets with the ultimate goal of accurate diagnosis as well as sufficient material for comprehensive predictive testing. Nonetheless, “traditional” cytological investigations such as bronchial washings, brushings, and lavages are still carried out for investigation of both suspected neoplastic and non-neoplastic conditions, and all these procedures still produce specimens in which florid benign cells mimic malignancy, while truly neoplastic cells lurk quietly in the background. Furthermore, even when neoplasia is not suspected, issues in preparation and interpretation may render a final assessment inaccurate and, therefore, clinically unhelpful or misleading. In this overview, we have tried to adopt a format partly modelled on the passage of a specimen from clinical acquisition to laboratory endpoint, thus taking in potential pitfalls in communication, clinical interaction, transport, and clinic-based preparation, as well as in morphology, immunocytochemistry, and suitability for predictive testing. It is not exhaustive but highlights areas that may frequently be encountered or are part of our personal experience. <b><i>Summary:</i></b> The account highlights potential pitfalls in respiratory cytopathology at key stages of the process from acquisition to reporting and presents these in both flow diagram and tabular form. We hope this is useful for the increasingly collaborative roles of cytotechnologist and cytopathologist and their wider involvement in the clinical investigative teams. <b><i>Key Messages:</i></b> Correct clinical and radiological information is crucially important and promotes the correct acquisition and processing of cytopathological specimens. Cross-discipline collaborative working ensures the most efficient use of the specimen such that diagnoses and predictive tests are performed on optimal material, reducing the potential for misinterpretation. Nonetheless, even with optimal material, morphological mimics and atypical antigen expression may mislead and render accurate diagnosis challenging.