After the
Republic of Macedonia's independence, he became a member of the political party
VMRO-DPMNE in 1992. He led its foreign relations commission for six years, as well as serving as the Chief of Staff of the Mayor of
Kisela Voda from 1997 to 1998. Trajkovski became the deputy foreign minister following VMRO-DPMNE's victory in the
1998 elections. In the presidential election, there were irregularities, so there was a partial re-run in December and Trajkovski managed to win 96 per cent of the vote.
OSCE's observers expressed "serious concerns" about the result, while domestic opposition politicians accused Trajkovski of unfairly mobilising groups of ethnic Albanians to vote multiple times and intimidate opposition supporters. Trajkovski's tenure was marked by tensions between
ethnic Macedonians and the republic's large
ethnic Albanian minority. The aftermath of the Kosovo War led to months of
conflict in 2001 between Macedonian security forces and ethnic Albanian rebels. During the conflict,
protests occurred due to the
Macedonian assault on
Aračinovo being halted, the evacuation of around 500
Nаtional Liberation Army insurgents, and the involvement of the
international community. Protesters broke into the parliament building and demanded to talk to him, shouting "treason" and "resignation." Although his powers were limited and his role largely ceremonial, he presided over the
NATO-brokered
Ohrid Framework Agreement (OFA) in 2001 that ended the violence and prevented a full-blown civil war in the Republic of Macedonia. He was also a signatory of OFA. He supported OFA and Macedonia's integration into NATO and the
European Union (EU). In his last act as president, he signed Macedonia's application for EU membership. == Death ==