A medical instrument holding apparatus includes a supporting mechanism, a moving mechanism, a basal portion and a counterweight. The supporting mechanism supports a medical instrument. The moving mechanism which has first and second sides, and a shaft portion located between the first and second sides. The moving mechanism supports the supporting mechanism, allowing the medical instrument and the supporting mechanism to be moved around the shaft portion. The basal portion is coupled to the shaft portion. The basal portion supports the moving mechanism, allowing the moving mechanism to rotate around the shaft portion. The counterweight is located on the second side of the moving mechanism. The counterweight generates a first rotation moment being smaller than a second rotation moment generated from the weights of the medical instrument and the supporting mechanism and acting around the shaft portion in the opposite direction to the second rotation moment.