There is a need for a fast and non-invasive tool to detect Pseudomonas aeruginosa airway colonisation in cystic fibrosis (CF) patients unable to expectorate. Fifty CF children and 19 controls aged 5–17 years were included in the feasibility study. A surface-enhanced Raman spectroscopy (SERS) nanochip optimised for detection of trace amounts of the P. aeruginosa biomarker hydrogen cyanide (HCN) was mounted inside a Tedlar bag, which the patient breathed into. The SERS chip was then analysed in a Raman spectrometer, investigating the C≡N peak at 2131 cm-1 and correlated with sputum cultures. One new P. aeruginosa colonisation occurred during the trial period. The C≡N peak intensity was enhanced in this sample in contrast to the subject's 3 other samples. Three additional patients had intense C≡N SERS signals from their breath, but no P. aeruginosa was cultured from their sputum. It is concluded that SERS spectroscopy can be developed into an easy to use hypersensitive clinical prescreening method for detection of HCN in human breath.