The year after winning the EuroLeague, in 2000, Žalgiris suffered one of its worse seasons. The club was eliminated after the group stage in the EuroLeague, finishing third in the NEBL and losing the LKL finals to Lietuvos Rytas for the first time. In the 2001 season, the team reached the new EuroLeague playoffs, but lost to AEK. Žalgiris regained the LKL championship, beating Lietuvos Rytas 3–2. The 2002 season was again disappointing, as the team was eliminated in the EuroLeague after the group stage and lost the LKL championship. In the 2003 season, they were again eliminated in the EuroLeague playoffs, but achieved the LKL championship, beating Lietuvos Rytas 4–2.