Voters headed to polling stations to chose between Mr Mubarak and his nine rivals, most of them little-known leaders of political parties with few members, with the exception of two liberal candidates, Ayman Nour and Noman Gomaa.
Several hundred demonstrators gathered in central Cairo to call for an election boycott, but plainclothes men broke up the protest and beat up some activists. The government had banned demonstrations on Wednesday.
Mr Mubarak, 77, has won office four times since 1981 through referendums in which he was the single candidate, chosen by a parliament dominated by the ruling National Democratic Party.
He changed the system this year after the United States and Egyptian protest groups pressed for reform.
The election enlivened political debate after decades of stagnation and brought criticism of Mr Mubarak almost unthinkable a year ago.
But the power structure remains the same and the opposition say they doubt Mr Mubarak wants real political change.
“This is not an election. They are treating this as another referendum. The government has lied (about a fair vote),” said Ayman Nour, 40, running for the Ghad Party.
COMPLAINTS: Mr Nour told a news conference that the ruling party and municipality officials were paying people either 20 or 50 pounds ($3 or $9) to vote and that the ink used on people’s fingers to prevent them voting again was not indelible.
The Egyptian Organization for Human Rights, the main independent rights group, made the same allegation of buying votes, but it was not possible to corroborate the reports.—Reuters