Boris Trajkovski had been flying to an investment conference in Mostar when his plane crashed in mountains in the south of the country.
The government plane, which was also carrying six other officials, came down in heavy rain and fog.
Trajkovski, 47, was elected president of the former Yugoslav republic in 1999.
His term was marked by tensions between Slavic-speaking Macedonians and the country's large ethnic Albanian minority.
But he won praise for cutting a deal in 2001 that averted civil war, and he was viewed in the West as a moderate leader keen to bring his country into the European fold.
Boris Trajkovski was born in 1956 in Strumica. He studied law at Skopje's Saint Cyril and Methodius University and made several study visits to the United States.
He was also a lay preacher in the Methodist Christian church, a minority faith in the predominantly Orthodox and Muslim country.
"The Balkan region today still is not safe, it is not yet a place of decent life. We are surrounded by a large arsenal of weapons, a large number of people who are getting rich through smuggling, corruption, and murder."
Until 1997 he headed the legal department of a construction company.
That year he became chief of the cabinet of the mayor of Skopje's Kisela Voda municipality.
In January 1999, his career in politics began when he was appointed deputy minister of foreign affairs.
When he was elected president later that year, he promised to serve all citizens regardless of ethnicity. He soon faced two big challenges in fulfilling that promise.
The first came during Serbia's crackdown on ethnic Albanians in neighboring Kosovo, when hundreds of thousands of ethnic Albanian refugees fled across Macedonia's border.
Trajkovski accused NATO of paying too little attention to the ethnic tensions brewing in Macedonia, and the influx of the ethnic Albanian refugees.
In 2001, those tensions threatened to boil over into civil war, following months of armed clashes between Macedonian forces and ethnic Albanian guerillas.
But that year Trajkovski presided over a NATO-brokered peace deal that gave ethnic Albanians greater political and language rights in return for rebel disarmament. It also allowed for peacekeeping missions from NATO and, later, the European Union.
The deal won Trajkovski praise abroad. Last year, he commended the "timely" intervention of NATO and the European Union.
"When a conflict is resolved peacefully and no longer makes newspaper headlines, it is sometimes quickly forgotten. But the ceaseless efforts made by [EU Commission President] Romano Prodi, [EU foreign policy chief] Javier Solana, [EU External Relations Commissioner] Chris Patten, and [former NATO chief] Lord Robertson deserve to be remembered as one of the most successful and timely interventions ever undertaken by the European Union and by NATO," Trajkovski said.
During a visit to RFE/RL in late 2002, he also spoke of some of the other major problems facing Macedonia and its Balkan neighbors.
"The Balkan region today still is not safe, it is not yet a place of decent life. We are surrounded by a large arsenal of weapons, a large number of people who are getting rich through smuggling, corruption, and murder," Trajkovski said.
Trajkovski said that joining the European Union was Macedonia's most important goal.
It was a theme of his last public speech, made yesterday. "We, ourselves have to be guarantors that the Republic of Macedonia will soon become a member of the European Union. I would like to point out one fact which very much pleased me and encouraged me today: the representatives of all the political parties and the Macedonian people, regardless of any ethnic or political belongings, regardless of any religious or political preferences, stand behind [Macedonia's] application [for EU membership]," he said.
Today was to have been a milestone in reaching that goal.
Macedonian Prime Minister Branko Crvenkovski was to formally submit the country's application for EU membership at a ceremony in Dublin. But after news of the plane crash came in, the ceremony was canceled and Crvenkovski flew back to Skopje.
Trajkovski is married with a son and daughter.