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Hajduk entered the new millennium by winning their fourth Croatian title, led by coach Zoran Vulić and featuring mostly "homegrown" players from the club's academy. The league concluded in a six-team play-off, where Hajduk stepped up their game after coming second, five points behind Dinamo, during regular season. Eight victories, an away draw in Koprivnica and a minimal loss to Dinamo saw the Whites reach the top. The excitement peaked on the last matchday, an away game in Varaždin. The small northern town was flooded with thousands of Hajduk fans from all over Croatia, some coming even from abroad. The Whites' 4-2 victory sparked massive celebrations in Split.
The Champions League qualifying opened with a penalty-shootout progression past Ferencvaros of Hungary. Unfortunately, Real Mallorca proved too strong in the following round. The first leg at Poljud was won by 1-0 courtesy of a Mate Bilić free kick, but the Whites lost the second leg 0-2 in extra time.
Another "sun," as the Croatian Cup trophy is known for its appearance, landed at Poljud the following season. Uljanik of Pula was brushed aside in a two-leg final with 1-0 and 4-0 respectively.
Coach Zoran Vulić returned to the helm in the season 2003/04. The championship started with a convincing sequence of victories, and the Whites were first in the standings after regular season. The team maintained their good form throughout the playoffs, and the title was once again celebrated against Varteks of Varaždin, this time after a 2-0 home victory at Poljud.
The same opponent returned for the championship-deciding game of the following campaign. Hajduk opened the 2004/05 season with Ivan Katalinić as head coach, however the surprising defeat to Shelbourne of Ireland in the Champions League qualifying saw him replaced with Blaž Slišković. He led the team to a first-place finish in the winter break. The January transfer window featured the sensational acquisition of Niko Kranjčar, which generated widespread euphoria on the eve of the spring season finale. With just a few rounds remaining, sport director Igor Štimac, together with the more experienced Petar Nadoveza, took over the reins from Slišković and guided the team to a sixth Croatian title. The team from Varaždin was aptly overcome by a six-nil scoreline.
The opening of the following season was marked by another coaching change, the iconic Ćiro Blažević being brought in, but also by a disastrous European elimination at the hands of Hungary's Debrecen – 0-3 and 0-5.
The club's uncertain financial prospects had become a very serious problem around this time. In early 2008 Hajduk was facing bankruptcy. The law came to Hajduk's rescue: by the ordnances of the Sporting Act, the club was transformed into a sporting joint-stock company.
Fans purchased many shares, with additional financing coming from the City of Split and a consortium of local businessmen. Hajduk was thus registered as the first sporting joint-stock company in Croatia.
Material from publications by Jurica Gizdić used with permission: Hajduk in Official Competitions, 100 Years of Hajduk, Hajduk's Presidents and Hajduk's Coaches. The History of Hajduk by decades was prepared by Dag Baldasar.