The present invention relates to an automated centrifuge system for automatically centrifuging liquids containing biological materials such as nucleic acids using a general centrifuge. The automated centrifuge system of the present invention comprises a centrifuge including a rotor in which at least two swing buckets with at least two microplates mounted thereon are provided so as to perform centrifugation of the liquids, a multi-joint robot with at least three joints which includes a gripper attached to a final arm thereof and a finger attached to the gripper, and a controller for controlling the predetermined procedures and the operation of the robot. In particular, the centrifuge and the multi-joint robot are disposed close to each other on a rigid bottom plate. A sensor for use in position detection is attached to the gripper or finger. At least one marker is attached at a predetermined position on a central frame of the rotor, and the predetermined position is spaced apart from a rotating shaft of the rotor by a predetermined radial distance. The controller causes the gripper to be moved so that the sensor is placed onto a circumference of a circle having a radius equal to the predetermined radial distance and the gripper to be moved around an axis of the rotating shaft of the rotor so that the sensor can detect a position of the marker, thereby automatically performing the predetermined procedures through the detection of positions of the microplates mounted to the swing buckets of the centrifuge. According to the automated centrifuge system of the present invention, the angular positions of the microplates or test tubes in the rotor of the centrifuge placed at arbitrary angular positions before or after the centrifugation can be correctly detected. Thus, the centrifuging procedures can be automatically performed in any kinds of conventional centrifuges. Furthermore, since the overall operation of the automated centrifuge system is simplified, the production costs of the automated centrifuge system can be remarkably reduced and reliability of the system can also be greatly improved.