The polling stations opened in the morning amid tight security for the final phase of a tumultuous transition overseen by the increasingly unpopular ruling military council.
Last evening, voting hours were extended by one hour due to a surge in turnout, which Presidential Elections Commission's Secretary General Hatem Bagato said was "magnificent and more than the expected".
The Interior Ministry today said all filled ballot boxes are being kept under tight security.
The historic two-day presidential election is being contested by candidates with both Islamist and secularist leanings who have promised radically different futures for the country.
Fifty million people are eligible to vote. A total of 13 contenders are in the fray but the race boils down to five major names.
Two figures of the former regime --former foreign minister Amr Moussa and former prime minister Ahmad Shafiq, are up against two Islamists -- Mohamad Morsi from the Muslim Brotherhood and Muslim Brotherhood-defect Abd-al-Munim Abul Futtuh, and leftist front-runner Hamadin Sabahi.
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The military council which assumed presidential power in February 2011 has promised a fair vote and civilian rule.
The election pits Islamists against secularists, and revolutionaries against Mubarak-era ministers.
If no candidate gets an absolute majority, the top two vote-getters would compete in a run-off on June 16 and 17. The winner of the run-off would become Egypt's first post-Mubarak era president and will take office before July 1.
The elections are being conducted under full judicial supervision and international monitors have arrived to observe the transparency of the process.