Cystic fibrosis (CF) gut manifestations are predominantly secondary to cystic fibrosis transmembrane regulator protein (CFTR) dysfunction. The CFTR gene is expressed throughout the intestinal tract. Because the intestine is difficult to assess in humans, there exists a lack of data on the underlying mechanisms of intestinal dysfunction. A more tractable approach involves the use of mouse models of CF, created by gene targeting techniques, to describe the consequences of CFTR dysfunction in the intestinal tissues, including mucus accumulation, disturbed motility, small bowel bacterial overgrowth and inflammation with altered innate immune responses, that are likely to be interrelated. We will focus on the latter. Recently, in people with CF, even in the absence of overt gastrointestinal symptoms, chronic intestinal inflammation and abnormal balance of the microbiota have been evidenced. Because chronic gut inflammation may be a driver for systemic inflammation, the prevention and control of intestinal inflammation represents a promising research strategy.This article is part of a Directed Issue entitled: Cystic Fibrosis: From o-mics to cell biology, physiology, and therapeutic advances.