Abstract: An automatic capillary replacement system includes a base on which a clamping loader is detachably mounted. A main stage is disposed on the base so as to reciprocate horizontally along the X axis. A sub-stage is disposed on the main stage so as to reciprocate horizontally along the Y axis. A capillary mounting unit is mounted on the sub-stage so as to reciprocate horizontally along the Z axis. A new capillary to be supplied is mounted on the capillary mounting unit. A capillary collecting/supplying unit has a capillary clamper which is movable on the main stage along the X, Y and Z axes. An unclamping unit is disposed on the sub-stage, and selectively releases a clamping part of the clamping loader so that the capillaries can be separated and mounted. First to third drive parts drive the main stage, the sub-stage and the capillary collecting/supplying unit to reciprocate.