Cystic fibrosis (CF) is a genetic chronic condition characterised by aberrant mucosa and localised and systemic inflammation, which affects mainly the respiratory and digestive systems secondary to dysfunctional epithelial electrolyte and water transfer. The gut microbiota in CF is distorted in comparison with healthy controls. This includes elevation of potentially pathogenic Proteobacteria or its sub-rank taxa, and suppression of taxa belonging to the phyla Firmicutes, Bacteroidetes, and Actinobacteria, which predominant in the gut microbiota and play important roles in the regulation of host metabolism and immune functions in the general population. The gut dysbiosis in CF has been linked to disease manifestations in the respiratory and gastrointestinal systems. Indirect evidence from the general population and CF animal studies implies a role of gut microbiota in the pathogenesis and/or management of other CF co-morbidities associated with metabolism and inflammation, such as CF-related diabetes (CFRD), colorectal cancer, malnutrition and overweight/obesity. Among a variety of host and environmental factors that can influence the gut microbiota, diet seems to be the most modifiable. Therefore, the present study investigated the associations between gut microbiota and diet (macronutrients, micronutrients, food groups and flavonoids), as well as clinical characteristics important in CF management (e.g. lung function, body composition and psychological status), in the group of free-living adults with CF.