He was a devout Muslim who fought for the emancipation of his people within a multi-ethnic state, but never realised his dream of a reunified Bosnia.
Izetbegovic long advocated a state in which ethnic Muslims, Croats and Serbs would fully enjoy their national and religious rights, denied in former communist Yugoslavia.
But seven years after the 1992-1995 war, his country remains divided along ethnic lines and is struggling to recover.
He was a key figure during the war in Bosnia when about 200,000 people died and more than two million were forced out of their homes.
He won worldwide sympathy by running the government from sandbagged buildings during the three-and-a-half-year-long siege of Sarajevo by Bosnian Serbs, under constant threat from their artillery and sniper attacks.
The short, blue-eyed Muslim walked to his office through the bombardment, believing, according to those who knew him, that death would come when Allah willed it.
Together with the then Croatian president Franjo Tudjman and former Serbian strongman Slobodan Milosevic, Izetbegovic participated in marathon peace negotiations in the US city of Dayton, Ohio, in November 1995, led by the US diplomat Richard Holbrooke. These resulted in a peace accord for Bosnia.
The deal split the country into the two highly autonomous entities of the Serbs' Republika Srpska and the Muslim-Croat Federation and brought in NATO-led peacekeepers to maintain security.
"This is not a just peace, but it is more just than continuation of the war," Izetbegovic told his people after signing the accord. "In the situation as it is, and in the world as it is, a better peace could not be achieved."
Father of Bosnian Muslims
Izetbegovic said in an interview he considered his greatest achievement to be the fact that Bosnia never fell under Milosevic's regime.
"In the situation as it is, and in the world as it is, a better peace could not be achieved"
Alija Izetbegovic on the Dayton Peace Treaty, 1995
In the postwar period, Izetbegovic filled the Muslim seat in the tripartite presidency that also included a Croat and a Serb member.
But in October 2000, his encroaching age and failing health forced him to step down from the presidency, after he was weakened by two heart attacks.
Last year he also stepped down as head of his Muslim nationalist Party of Democratic Action (SDA), remaining its honorary president.
He was fitted with a pacemaker by Slovenian cardiologists in 2002. Thereafter, Izetbegovic rarely appeared in the media.
His wartime charisma began to fade amid criticism that the country's economic situation was failing to improve, leaving the country dependent on foreign aid.
Izetbegovic (L) with peace prize
winner Elie Wiesel in 1992
There was further criticism that he had failed to clear corrupt individuals out of Muslim-dominated sections of the administration.
Bosnian Serbs also claimed Izetbegovic was responsible for war crimes committed by Muslim forces. They provided documents to the United Nations tribunal in The Hague in an attempt to have him formally indicted, but the tribunal has yet to respond.
The international community, deeply involved in the Bosnian peace process, also accused Izetbegovic's party, the SDA, of trying to dominate the multi-ethnic state.
Meanwhile, Izetbegovic claimed the international community had tried to reduce the influence of Muslims, who make up more than 40% of the country's population.
Father of the nation
Born on 8 August, 1925 in the northeastern town of Bosanski Samac, Izetbegovic moved to Sarajevo with his family at the age of three.
"The West is not rotten. Islam is the best, that is true, but we are not the best. Instead of hating the West, let us compete with it. Let's have a dialogue with it"
Alija Izetbegovic, 1997
Much of his adolescence was spent under Nazi occupation.
Izetbegovic served two prison terms totalling nine years in communist Yugoslavia because of Islamic activism. He was never a member of the Communist Party.
He was released in 1988 and less then a year later he co-founded the SDA, which won the 1990 elections along with Serb and Croat nationalist parties.
After the elections, Izetbegovic was appointed Bosnia's president.
In 1992, the country declared independence, following in the footsteps of Slovenia and Croatia, sparking the war with pro-Belgrade Bosnian Serbs.
Izetbegovic, who like other Bosnian Muslims practised a liberal form of Islam, said on many occasions he had never wished to create an Islamic state in Bosnia, stressing his ultimate support for a multi-ethnic country.
In a passage of an "Islamic Declaration" whose 1970 publication eventually earned him his second conviction in 1983 and was often used by Serbs and Croats as justification for the war, he wrote: "There can be no peace or co-existence between Islamic faith and non-Islamic political institutions."
The tract was seen by the communist authorities in Yugoslavia as a call for the imposition of Sharia law in Bosnia-Hercegovina - then a Yugoslav republic.
In 1997, however, he told an Islamic conference in Tehran that "the West is not rotten. Islam is the best, that is true, but we are not the best. Instead of hating the West, let us compete with it. Let's have a dialogue with it."
He was legal counsel to two Sarajevo firms before entering politics full-time in his mid-sixties.
The fact that he was a newcomer to politics was seen by many as the reason for what was perceived as his indecisiveness and lack of diplomatic skills.
"Dedo" (grandpa), as he was known to many Bosnian Muslims for his father of the nation role, was reportedly separated from his wife and lived modestly.
Alija Izetbegovic died on Sunday aged 78. He had two daughters and a son.