For AFSOUTH the year 2000 was mainly marked by completing the transition into the new command structure and by a progressively increased engagement in Balkan operations. As the staffing headquarters for KFOR, AFSOUTH conducted a series of major programs to bring new teams rotating into key staff positions at KFOR up to the required standards of interoperability. This mission had particular relevance when a non-NATO headquarters, Eurocorps, was nominated to provide the core staff for KFOR headquarters (KFOR staff rotated every six months, with a single headquarters identified a constituting the core). Even though it was made up of personnel from NATO nations, Eurocorps is not part of the NATO structure and required familiarisation with NATO procedures as well as with the Kosovo operational environment. Not less demanding was the task to 'mount' the KFOR rotating headquarters, which was formed from within Southern Region headquarters, mainly from JCS of Verona and JCSE of Izmir. In this case the additional challenge was to integrate a staff coming from different headquarters even though they were already familiar with basic NATO procedures. This mission facilitated the selection as the next COMKFOR the AFSOUTH Chief of Staff, Lt.Gen. Carlo Cabigiosu, the first Italian officer assigned to this key position.
Meanwhile, the exercise program received new impetus and was able to achieve major successes. Among the yearly exercises, like the Anti-submarine Warfare exercise "Dogfish" and the air exercise "Ample Train" (conducted at Solenzara, France), the most complex was certainly "Destined Glory." This saw Greek forces training on Turkish soil for the first time in decades. AFSOUTH also conducted the most challenging biannual exercise "Dynamic Mix". This exercise marked several 'firsts.' Conducted in Greece, Turkey and the Eastern Mediterranean, it was characterised by the presence -- after several decades – of Turkish air and ground forces during training activities in Greece. It was also the first southern region exercise in which Hungary and the Czech Republic participated as NATO members, and the first major AFSOUTH exercise conducted after the adoption of the new military structure.
The PfP training program also saw new improvements, with the maritime and amphibious exercise "Co-operative Partner" conducted for the first time in the Ukraine; exercise "Co-operative Best Effort" in Romania; exercise "Co-operative Dragon" in Albania and the air exercise "Co-operative Key" in Romania. Also, "Co-operative Determination" was the first computer-assisted, command-post PfP exercise ever conducted in Switzerland.
The natural outcome of the reasserted role of AFSOUTH was the NATO Council's decision to modify the command and control structure for Balkan operations, giving AFSOUTH complete operational responsibility of the NATO-led operations in Bosnia-Herzegovina and in Kosovo. This decision, which was to be gradually implemented the following year, was an important step to guarantee a more efficient use of the operational resources. For several years land-component commanders of Balkan operations had reported directly to SACEUR, while operational command of the air and maritime components remained with AFSOUTH and its component commands. At the same time, by passing down most of the responsibilities for Balkan operations, SHAPE was better able to concentrate on its strategic mission. As a consequence, the last few months of the century were mainly spent by AFSOUTH staff in progressively accelerating preparations for a seamless transition into the new command and control structure for Balkan operations.