Background Respiratory pathogens from CF patients can contaminate inpatient settings, which may be associated with increased risk of patient-to-patient transmission. Few data are available that assess the rate of bacterial contamination of outpatient settings. We determined the frequency of contamination of CF clinics and the effectiveness of alcohol-based disinfectants in reducing hand carriage of bacterial pathogens. Methods We conducted a point prevalence survey and before–after trial in outpatient clinics at 7 CF centers. The study examined CF patients with positive respiratory cultures for Pseudomonas, Staphylococcus, Stenotrophomonas or Burkholderia species. Hand carriage and environmental contamination with respiratory pathogens were assessed during clinic visits (Part I) and the effectiveness of hand hygiene performed by CF patients (Part II) was determined using molecular typing of recovered isolates. Results In Part I ( n = 97), the contamination rate was 13.6%. Pseudomonas and S. aureus, including methicillin-resistant strains, were cultured from patients' hands (7%), the exam room air (8%), and less commonly, environmental surfaces (1%). In Part II ( n = 100), the hand carriage rate of pathogens was 13.5% and 4 participants without initial detection of pathogens had hand contamination when recultured at the end of the clinic visit. Conclusions Respiratory pathogens from CF patients can contaminate their hands and the clinic environment, but the actual risk of patient-to-patient transmission in the outpatient setting remains difficult to quantify. These findings support several recommendations CF infection control recommendations including hand hygiene for staff and patients, contact precautions for certain pathogens, and disinfecting equipment and surfaces touched by patients and staff.