A substrate transfer system is used in fabricating a liquid crystal display (LCD) device. The system includes a cassette having a bar code, a cassette stocker to store the cassette; an auto guided vehicle that is able to transfer the cassette; a moving path unit to determine a moving path of the auto guided vehicle, a plurality of process stages at which processes are conducted on a substrate during fabrication of the LCD device, and a host to control the cassette stocker, the auto guided vehicle and the process stages. At least one of the auto guided vehicle and the cassette stocker having a bar code reader.