Derived from instinct, intuition, or an ingrained inclination.
He understood in his bones that the odds were not in his favor.
She could feel the rhythm in her bones.
Used other than figuratively or idiomatically: see in, one's, bones: especially, referring to rheumatic aches sensitive to atmospheric pressure, temperature, and humidity.
As his aging hands became increasingly arthritic, he would often tell us that he could feel it in his bones when a snowstorm was coming.