Assad is facing two little-known challengers and is expected to win a crushing victory despite the three-year-old civil war which the United Nations has warned is likely to drag on even longer as a result of the election.
There was no voting in the roughly 60 per cent of the country outside the control of Assad's government, which includes large areas of second city Aleppo.
But polling was held in the heart of third city Homs, in ruins after rebel forces pulled out early last month following a devastating two-year siege in a boost for the president whose family has held power in Syria for more than 40 years.
The capital is firmly under the government's control but comes under periodic rebel bombardment from the suburbs, and the Syrian Observatory for Human Rights reported that several neighbourhoods came under fire today.
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Billboards glorifying Assad cover the streets of Damascus although inside polling stations photographs of his two challengers - Hassan al-Nuri and Maher al-Hajjar - had been put up alongside the president's.
None of the voters questioned by AFP said they had voted for the challengers.
Hind al-Homsi, 46, said she had made a small cut in her finger and left a bloody fingerprint on the circle underneath Assad's name.
In the central city of Homs, security forces deployed in strength a day after a truck bomb killed 10 people in the nearby countryside.
The interior ministry said more than 15 million Syrians were eligible to vote, adding to the 200,000 who already cast votes abroad last week.
At least 162,000 people have been killed in Syria since an uprising against Assad's rule erupted in March 2011, and nearly half the population have fled their homes.
Foreign governments allied to Assad - Iran, North Korea and Russia - sent observers to monitor the election, but Western governments have dubbed it a mockery of democracy.