Mesić was elected President of the Republic of Croatia in the 2000 election after winning the first round and defeating Dražen Budiša of HSLS in the second round.
Mesić ran as the joint candidate of the HNS, HSS, LS and IDS.
He received 41% of the vote in the first round and 56% in the second round.
After becoming president, he stepped down from membership in the HNS.

He heavily criticized former President Franjo Tuđman's policies as "nationalistic and authoritarian", lacking a free media and employing bad economics, while Mesić favored a more liberal approach to opening the Croatian economy to foreign investment.
In September 2000 Mesić retired seven Croatian active generals who had written two open letters to the public arguing that the current government administration "is campaigning to criminalize Homeland War and that the Government is accusing and neglecting the Croatian Army".
Mesić held that active duty officers could not write public political letters without approval of their Commander-in-Chief.
Opposition parties condemned this as a dangerous decision that could harm Croatian national security.
Mesić later retired four more generals for similar reasons.

As president, Mesić was active in foreign policy.
Mesić promoted Croatia's ambition to become a member of the European Union and NATO.
He also initiated mutual apologies for possible war crimes with the President of Serbia and Montenegro.
After Constitutional amendments in September 2000, he was deprived of most of his roles in domestic policy-making, which instead passed wholly to the Croatian Government and its Premier.

Mesić testified at the International Criminal Tribunal for the Former Yugoslavia that implicated the Croatian army in the war in Bosnia and Herzegovina.
The right-wing parts of the Croatian public took issue with this, saying that his testimony contained untrue statements and questioned his motives (he was often branded "traitor"), and noting that much of his testimony occurred before his presidency, as an opposition politician.
His denunciation of the assassination of Serbian Prime Minister Zoran Djindjic on 12 March 2003 marked a notable thawing of relations with Serbia, and he attended his funeral in Belgrade.

He opposed the United States' military campaign against Iraq and Saddam Hussein's regime without gaining United Nations approval or mandate beforehand.
Immediately following the invasion of Iraq on 20 March 2003, Mesić deplored that by attacking Iraq, the Bush administration had marginalized UN, induced divisions in EU, damaged relationships with traditional allies, disturbed the foundations of international order and incited a crisis, which could spill over the borders of Iraq.

Mesić improved Croatian foreign relations with Libya by exchanging visits with the Libyan leader Muammar al-Gaddafi, contrary to the wishes of U.S. and British diplomacy.

The first of Mesić's mandate was not marked with historically crucial events like the Tuđman presidency had been, Croatia's public political orientation shifted away from the HDZ, mostly to the benefit of leftist parties.
When the government changed hands in late 2003, problems were expected between the leftist President and a Government with rightist members, but Mesić handled the situation gracefully and there were few notable incidents in this regard.
He served his first 5-year term until February 2005.
In the 2005 election, Mesić was a candidate supported by eight political parties and won nearly half of the vote, but was denied the absolute majority by a few percent.
Mesić faced off with Jadranka Kosor in the run-off election and won.
He served his second 5-year term until 2010 when he was superseded by Ivo Josipović.

On 1 March 2006 the Civic Assembly of Podgorica, Montenegro's capital, decided to declare Mesić an honorary citizen.
The move was opposed by pro-Serbian parties in Montenegro.

In December 2006, a controversy arose when a video was published showing Mesić during a speech in Australia in the early 1990s, where he said that the Croats "won a victory on April 10th" (when the f
Mesić was elected President of the Republic of Croatia in the 2000 election after winning the first round and defeating Dražen Budiša of HSLS in the second round. Mesić ran as the joint candidate of the HNS, HSS, LS and IDS. He received 41% of the vote in the first round and 56% in the second round. After becoming president, he stepped down from membership in the HNS.
He heavily criticized former President Franjo Tuđman's policies as "nationalistic and authoritarian", lacking a free media and employing bad economics, while Mesić favored a more liberal approach to opening the Croatian economy to foreign investment. In September 2000 Mesić retired seven Croatian active generals who had written two open letters to the public arguing that the current government administration "is campaigning to criminalize Homeland War and that the Government is accusing and neglecting the Croatian Army". Mesić held that active duty officers could not write public political letters without approval of their Commander-in-Chief. Opposition parties condemned this as a dangerous decision that could harm Croatian national security. Mesić later retired four more generals for similar reasons.
As president, Mesić was active in foreign policy. Mesić promoted Croatia's ambition to become a member of the European Union and NATO. He also initiated mutual apologies for possible war crimes with the President of Serbia and Montenegro. After Constitutional amendments in September 2000, he was deprived of most of his roles in domestic policy-making, which instead passed wholly to the Croatian Government and its Premier.
Mesić testified at the International Criminal Tribunal for the Former Yugoslavia that implicated the Croatian army in the war in Bosnia and Herzegovina. The right-wing parts of the Croatian public took issue with this, saying that his testimony contained untrue statements and questioned his motives (he was often branded "traitor"), and noting that much of his testimony occurred before his presidency, as an opposition politician. His denunciation of the assassination of Serbian Prime Minister Zoran Djindjic on 12 March 2003 marked a notable thawing of relations with Serbia, and he attended his funeral in Belgrade.
He opposed the United States' military campaign against Iraq and Saddam Hussein's regime without gaining United Nations approval or mandate beforehand. Immediately following the invasion of Iraq on 20 March 2003, Mesić deplored that by attacking Iraq, the Bush administration had marginalized UN, induced divisions in EU, damaged relationships with traditional allies, disturbed the foundations of international order and incited a crisis, which could spill over the borders of Iraq.
Mesić improved Croatian foreign relations with Libya by exchanging visits with the Libyan leader Muammar al-Gaddafi, contrary to the wishes of U.S. and British diplomacy.
The first of Mesić's mandate was not marked with historically crucial events like the Tuđman presidency had been, Croatia's public political orientation shifted away from the HDZ, mostly to the benefit of leftist parties. When the government changed hands in late 2003, problems were expected between the leftist President and a Government with rightist members, but Mesić handled the situation gracefully and there were few notable incidents in this regard. He served his first 5-year term until February 2005. In the 2005 election, Mesić was a candidate supported by eight political parties and won nearly half of the vote, but was denied the absolute majority by a few percent. Mesić faced off with Jadranka Kosor in the run-off election and won. He served his second 5-year term until 2010 when he was superseded by Ivo Josipović.
On 1 March 2006 the Civic Assembly of Podgorica, Montenegro's capital, decided to declare Mesić an honorary citizen. The move was opposed by pro-Serbian parties in Montenegro.
In December 2006, a controversy arose when a video was published showing Mesić during a speech in Australia in the early 1990s, where he said that the Croats "won a victory on April 10th" (when the f
Stjepan Mesić