The balloting comes amid a devastating, three-year civil war that activists say has killed more than 160,000 people, about a third of whom were civilians. It's also Syria's first multi-candidate election in more than 40 years.
The opposition's Western and regional allies, including the US, Britain, France, Saudi Arabia and Turkey, have called the vote a farce.
The so-called internal Syrian opposition groups seen as more lenient are also boycotting the vote, while many activists around the country are referring to it as "blood elections" for the horrific toll the country has suffered.
Assad, who is running for a third seven-year term and whose re-election is all but a foregone conclusion, faces two government-approved challengers in the race, Maher Hajjar and Hassan al-Nouri, both of whom were little known in Syria before declaring their candidacy for the country's top post in April.
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At a polling station in the city's Dama Rose hotel, many voters refused to go behind the curtain to vote in privacy, instead publicly circling Assad's name.
At the same station in central Damascus, a box with pins was available for those who wanted to prick their finger and vote in blood, a symbolic act of allegiance and patriotism. Odai al-Jamounai, 18, said he voted with his blood "to express by my love to my country and my leader."
"He is the most competent to lead the country," Qadah said after casting his ballot. "We need a strong leader in these difficult times."
At least three flights from Kuwait, chartered by an anonymous Syrian businessman, were to bring Syrian expats home to vote.