From Wikipedia:
A gut feeling, or gut reaction, is a visceral emotional reaction to something, and often one of uneasiness. Gut feelings are generally regarded as not modulated by conscious thought. (For a discussion regarding the brain-gut connection, please see Irritable Bowel Syndrome, as well as literature discussing the physiologic manifestations of emotions i.e. neuroendocrine gastrointestinal physiology). Gut feelings come from within, what your brain tells you to do. It also allow you to make a decision based on what your "gut" tells you to do.
The phrase "gut feeling" may also be used as a short-hand term for an individual's "common sense" perception of what is considered "the right thing to do"; such as: helping an injured passerby, avoiding dark alleys and generally acting in accordance with instinctive feelings about a given situation. It can also refer to simple common knowledge phrases which are true no matter when said, such as "Water is wet", "Fire is hot", or to ideas that an individual intuitively regards as true, without proof (see "Truthiness" for examples).
Gut feelings, like all reflexive unconscious comparisons, can be re-programmed by practice or experience.

But...
In my experience, and after reaching a mature age, I think intuition and gut feelings are NOT unconscious reflexes, but instead are cultivated standards that are of use in deciphering emotional and physical and intellectual hazards or opportunities, to accomplish a reasonable understanding of how to handle one’s self in almost any situation, that’s consistent with the mind, heart, and spirit, of what it means to be sentient and involved with other Beings. It seems to me that a brain which manifests unresolved emotions as discomfort and disease, is more culturally handicapped than pathological.