Polls opened at 06:00 local Burundian time (04:00 GMT), for the long awaited presidential elections where incumbent President Pierre Nkurunziza is standing for a third term in presidency. On clashes Tuesday two people died overnight, including a police officer and a civilian, hours before the ballot boxes opened.
Several opposition parties have announced they will boycott the elections.
The elections came after a long night of explosions and gunfire in the capital Bujumbura. Gunfire and clashes continue on the streets, according to the BBC's correspondent Maud Jullien.
The opposition says Nkurunziza is only entitled for two terms as the constitution clearly stipulates.
"The government has opted to isolate itself and go ahead with pseudo-elections," prominent opposition figure Leonce Ngendakumana was quoted by the AFP, after a ‘last ditch’ reconciliation talks were mediated by Uganda, but later collapsed on Sunday.
Another opposition figure, Jean Minani, accused the government of being "very irresponsible".
"They have refused to save Burundi from sliding into an abyss," he said.
The bloody unrest over Nkurunziza’s third term bid sparked violent protests and plunged the country in an unprecedented crises since the end of the civil war in 2006, which killed over 300,000 people.
Tensions in Burundi have forced more than 150,000 people to flee this year to neighbouring African nations, according to al Jazeera, many fearing their country may again sink in dangerous unrest.
Protests started in April and a failed coup attempt was staged by army generals in May while the President was abroad, most of whom were later arrested after Nkurunziza returned to the capital to reclaim his office.
Seven candidates are challenging Nkurunziza, however they have had no significant impact, BBC’s correspondents say. There are over 3.8 million eligible voters in Burundi.
Nkurunziza's main rival, Agathon Rwasa, is registered as an independent candidate because his political party, the National Liberation Forces (Forces pour la Libération Nationale, FNL) is not recognised by the government.
A peace deal let Nkurunzıza to become a president in 2005, after he led a Hutu rebel group fighting the Tutsi dominated army.
Fighting between Burundi's Hutu majority and Tutsi minority has flared up regularly since the country gained independence from Belgium in 1962.