“Go with your gut” is a piece of advice given to me many years ago, somewhere in the middle of my business career. What my boss was trying to convey to me was to trust or follow my intuition, or instinct, as opposed to only basing my opinion or decision on a thorough analysis of the facts.
The idiom most likely originated from the anxious, or “bad,” feeling you get in your stomach when you know something is wrong.
I can remember thinking through things to make a decision in my 20s and 30s only to find out it was wrong, and instead of thinking with my head I should have gone with my gut. At the time I did not have enough confidence to trust my inner feelings.