An automatic calibration system for calibrating the parallelism between a printing plane of a 3D printer and a virtual plane on which the extruder of the 3D printer moves, to align the printing plane with the virtual plane on which the extruder moves, includes: at least one extruder, or a printing head on which the extruder itself is mounted, movable on a horizontal plane; at least one device for measuring the distance of the printing plane associated with the extruder or with a printing head; a movable printing plane along the vertical axis Z, the plane being equipped with at least three non-aligned actuators, which are controllable and operable independently of each other; a central control unit (MCU or PLC) of the calibration system and of all the parts thereof.