Troops and riot police were in position outside the parliament building, two days after the Muslim Brotherhood-dominated legislature was dissolved following a ruling by the Constitutional Court, which is close to the ruling Supreme Council of the Armed Forces.
Armoured personnel carriers stood near the interior ministry - round the corner from the Brotherhood's campaign headquarters.
However, the Brotherhood denied reports that MPs were being refused access to the building. A Brotherhood spokesman said Mohammed el-Katatny, the speaker and a senior Brotherhood official, had been allowed entry and was working from his office.
The voters have to choose between Mohammed Morsi, the leader of the Brotherhood's political front, the Freedom and Justice Party, and Ahmed Shafiq, a former general. Mr Shafiq was the last prime minister under President Hosni Mubarak, the dictator of three decades overthrown 16 months ago in what seemed at the time to be a democratic revolution.
Some voters, including those who took part in the revolution, said they still thought the election would be free and fair. "I chose Shafiq, even though it was very difficult to vote for him," said Hassan el-Samra, a 19-year-old student. But he summed up the topsy-turvy world of modern Egyptian politics by saying he was also preparing to go to Tahrir Square to protest against Mr Shafiq, should he win.
He and his father, Amr, who also voted for Mr Shafiq in the middle-class district of Mohandessin, said they preferred a Shafiq victory because if the Muslim Brotherhood won it would not be possible to protest at all.
"Shafiq is a person," Mr Samra senior said. "You can speak against a person. But if you speak against the Brotherhood you are speaking against the word of God, and you can't challenge that. It's like Iran."
Analysts and western diplomats believe that Mr Morsi, with his strong backing from the ordinary middle classes and the mosques, would win a fairly conducted contest. Ahmed Abdul-Ati, secretary-general of his campaign, claimed yesterday that an opinion poll for a semi-official think-tank had predicted a 69 per cent vote for Mr Morsi, but its publication had been blocked.
However, the Brotherhood claims that the army is buying votes - accusations countered by supporters of Mr Shafiq, who point to the Brotherhood's strong record of social support to poorer areas as a form of bribe.
The French-style two-round system has brought about a widely condemned result in which the two rivals in the run-off obtained less than half the votes in the first round between them, and are undoubtedly the two most distrusted of all the major candidates.
The votes of liberals, Leftists and independent Islamists who led last year's revolution were split between three other leading candidates.
Leading opposition activists called for "revolutionaries" to boycott the poll, or even better to spoil their ballot as a deliberate protest - a campaign that gathered steam after Thursday's ruling.
"Look, my hands are clean," said Hossam Hamza, 30, standing outside the same polling station as the Samras, referring to the absence of ink-stains with which citizens' fingers are marked to stop them voting twice. "If we can get two to three million people to join the boycott that would be good."
He said that the military would win either way when the votes are counted at the close of polling today. "If Morsi wins, there will be no transition of power. If Shafiq wins, it's a power transition within the army."
The dissolution of parliament means its powers return for the time being to the military council. There is as yet no constitution outlining what powers the newly-elected president will have, and many assume that they will be restricted by the military if Mr Morsi wins.
But if victory goes to Mr Shafiq, who once described Mr Mubarak as his "role model", there will be little to stop the renewed exercise of military power other than more street protests.
"Shafiq will have the support of all the force that surrounded Mubarak," said Sayed Mahfouz, a lawyer who voted for Mr Morsi. "But if Morsi wins, he will be handed 'power' but not real power until there is a constitution. Then they will just limit the power of the president."
By Richard Spencer, The Telegraph, June 6, 2012