Which came first? The chicken or the egg? This age-old story is one and the same when it comes to gut permeability and the havoc it can wreak on a person’s body. Does leaky gut cause discomfort in the GI tract or is discomfort in the GI tract causing the gut to leak? Let’s take a closer look: Leaky gut is not an actual diagnosis. It is a term used by doctors to describe the deterioration of the mucosal lining in the small intestine.