Prevalence of Aspergillus fumigatus, as well as other species, and factors associated with risk induced by fungal colonization are poorly defined in cystic fibrosis (CF). We set up a national prospective study to document this risk. As a pilot study, the fungal risk was determined for 21 CF adult patients in a multidisciplinary way: using clinical parameters, notifying treatment, determining fungal presence in sputum and documenting ABPA status. 16 (76%) patients presented with fungal presence in sputum. Aspergillus fumigatus and Candida albicans were the predominant species, but less common mould species such as Scedosporium apiospermum, or Exophiala dermatitidis were also recovered. Factors significantly associated with fungal presence were pancreatic insufficiency, malnutrition, bacterial colonization, and corticosteroids. Candida albicans was correlated with more severe Shwachman Score, Pseudomonas aeruginosa colonization, and intravenous antibiotics use. Moulds species were significantly associated with inhaled corticosteroids. In conclusion, fungal presence in CF appears frequent and various, significantly associated with clinical data, such as inhaled corticosteroids and A. fumigatus. These results confirm the interest of the national prospective French study focused on 300 CF patients, in order to establish if patients could benefit from antifungal treatments or preventive measures.