Refers to the joints of the fingers; can be used for both the visible bumps and the internal joints.
My knuckles ache from the cold.
He has a habit of cracking his knuckles.
Compound of 指 (ゆび, 'finger') + の (possessive particle) + 節 (ふし, 'joint, node'). The reading ふし is the native Japanese word for a knot or joint.