Ukrainians turned out en masse in the capital Kiev and the west but in the east -- in the grip of a deadly pro-Russian insurrection for weeks -- most polling stations remained closed.
"The first thing we must do is bring peace to all the citizens of Ukraine," said billionaire tycoon Petro Poroshenko, the clear favourite in a packed field of candidates to lead the former Soviet republic.
"Armed people must leave the streets of towns and cities," he said after casting his ballot in Kiev.
The West regards the vote as crucial to prevent Ukraine from disintegrating further after Russia seized the Black Sea peninsula of Crimea in March in retaliation for the ouster of pro-Kremlin president Viktor Yanukovych.
Poroshenko called for "direct dialogue" with the people in Donetsk and Lugansk, where insurgents declared independence two weeks ago after referendums branded as shams by Kiev and the West.
'Ukraine another country'
But in the eastern regions regions, the hub of Ukraine's coal and steel industries, only nine of the 34 electoral constituencies were open, according to the central election commission.
"Ukraine is now another country so I don't see why we should take part in this election," said one woman in Donetsk who gave her name as Elisabeta.
Election officials had reported numerous cases of intimidation and attacks and rebels threatened on Saturday saying that they would disrupt the vote "by force if necessary".
In the centre of Donetsk, about 2,000 people demonstrated in support of the separatists, as armed men in camouflage gear and balaclavas lined the main square.
"You are heroes," the crowd shouted. "Do not take prisoners, kill them."
No fighting between rebels and Ukrainian forces was reported as voting was under way.
But violence flared on Saturday in the eastern flashpoint of Slavyansk, where one Italian photographer was killed and a French photographer and his Russian translator were wounded after being caught in a gun battle.
It was the first reported death of a journalist in east Ukraine, where one member of the Ukrainian defence force was also killed overnight.
Russian President Vladimir Putin, facing the threat of further Western sanctions if Moscow interfered in the vote, appeared to make a major concession on Friday by saying he was ready to work with the new Kiev team.
"We understand that the people of Ukraine want their country to emerge from this crisis. We will treat their choice with respect," he said.
Russia also said it started withdrawing from Ukraine's border around 40,000 soldiers whose presence had raised deep suspicions about Russia's next move.
But in a fresh sign of Moscow's plans to continue exerting pressure, Prime Minister Dmitry Medvedev announced plans on Sunday to visit Crimea, which has been formally incorporated as a part of Russia and where no voting was taking place.
Ukraine has mobilised more than 82,000 police and 17,500 volunteers to ensure security for the vote, being overseen by 1,200 international monitors.
Turnout about three hours after voting started was 17%, officials said.
New president needs 'legitimacy'
The interior ministry said 29,000 of the country's 33,500 polling stations had opened on time, with turnout particularly strong in Kiev, where 55-year-old housewife Nelia Issayenko said she was voting "so that Russia leaves us alone".
The election should give the new president a stamp of legitimacy as he or she battles against the insurgency and tries to repair relations with Ukraine's former masters in the Kremlin.
Opinion polls show Poroshenko winning 45% of the vote, just short of the 50% threshold needed to avoid a second round on June 15, and three weeks of further political uncertainty.
His main rival is former prime minister and heroine of the 2004 Orange Revolution Yulia Tymoshenko, who is trailing far behind on 7.5%.
The ballot was called by Kiev's interim leaders who took power after Yanukovych fled in the bloody climax of months of protests sparked by his rejection of a historic EU alliance.
The charred buildings and flower-heaped barricades still crisscrossing Kiev's Independence Square -- also the cradle of the 2004 Orange Revolution that first shook Russia's historic hold on Ukraine -- serve as poignant testimony to the more than 100 people killed in the bloody winter days.
At least 150 people have been killed in the east since the separatists took up arms against Kiev, while another 42 perished in fighting and a fire in the southern city of Odessa, according to an AFP tally based on UN and Ukrainian government figures.
Ukraine is hoping that up to $27 billion (20 billion euros) in global assistance it won after the old regime's fall may help avert threatened bankruptcy and revive growth in the recession hit country.
But the new leadership will also have to negotiate with Russia over vital supplies of gas, with Moscow threatening to halt shipments if Ukraine does not pay a bill by early June.
Voting closes at 1700 GMT, with first results expected from 2100 GMT.
"I hope this election will launch a process of change for the better... but I don't expect a magic wand," said Inna, a voter in the eastern city of Kharkiv that remains in Kiev's control.