Breath analysis in respiratory disease is a non-invasive technique which has the potential to complement or replace current screening and diagnostic techniques without inconvenience or harm to the patient. Recent advances in ion mobility spectrometry (IMS) have allowed exhaled breath to be analysed rapidly, reliably and robustly thereby facilitating larger studies of exhaled breath profiles in clinical environments. Preliminary studies have demonstrated that volatile organic compound (VOC) breath profiles of people with respiratory disease can be distinguished from healthy control groups but there is a need to validate, standardise and ensure comparability between laboratories before real-time breath analysis becomes a clinical reality. It is also important that breath sampling procedures and methodologies are developed in conjunction with clinicians and the practicalities of working within the clinical setting are considered to allow the full diagnostic potential of these techniques to be realised. A protocol is presented, which has been developed over three years and successfully deployed for quickly and accurately collecting breath samples from 323 respiratory patients recruited from 10 different secondary health care clinics.