The preparative Gas Chromatographic (GC) system for the JET Active Gas Handling System (AGHS) can separate a daily throughput of up to 20 moles of hydrogen isotope gas mixture into the pure products of T2, D2, and H2 with very small interfractions in between. Design, assembly and special parts of the GC system, the various steps of the gas chromatographic process including safety aspects, control system and results of the inactive commissioning are presented. The GC system fulfils its specifications for isotope separation. We also describe a simple program to calculate the hydrogen isotope profiles in the columns of the GC system.