Nebulisers are a potential source of bacterial contamination in cystic fibrosis (CF) patients. The aims of the study were to survey patient practice regarding maintenance of home nebulisers and to assess the impact of standardised guidelines derived from a previous in-vitro study. In total, 42 CF patients were studied. During two consecutive home visits, a questionnaire regarding routine patient practice was completed by a nurse while sputum and equipment samples were taken for bacteriological analyses. The first visit took place at baseline, and the second followed the implementation of detailed instructions for cleaning and disinfecting the nebulisers using a 0.5% hypochlorite solution. The first visit identified a great diversity in routine patient practices. Commensal bacteria, environmental bacteria and potential CF pathogens contaminated 78.5%, 57.1% and 14.3% of nebulisers respectively. After hypochlorite disinfection, rate and degree of global contamination decreased significantly, but the number of CF pathogens was not affected. There was no concordance between CF pathogens isolated from patients' sputum and their equipment. We conclude that in this sample of patients, initial routine practices were varied. With regard to CF pathogens, the superiority of a hypochlorite solution over a mix of other disinfection methods was not demonstrated.