The Effects of Stress on Your Digestive System There's a reason the digestive system is often referred to as the second brain in the body! This is because the gut has a system filled with neurotransmitters, even more so than the brain's central nervous system. When we experience stress, the brain activates the sympathetic nervous system known for producing the "fight or flight" response which prepares the body for danger by conserving other bodily functions that aren't needed, including digestion. When this occurs, the stomach slows down, and stress is placed on the large intestine, often causing stomach aches, gas, bloating, heartburn, nausea, and diarrhea.