Former Czech Prime Minister Milos Zeman faces Foreign Minister Karel Schwarzenberg in the second round.
People have braved freezing conditions to vote in what is proving a nail-bitingly close election.
Milos Zeman gained 24.2% in the first round, with Karel Schwarzenberg 23.4%.
“It’ll be very tight,” Karel Schwarzenberg said after casting his ballot in the small village of Sykorice, south-west of Prague.
“I’m not nervous, far from it, I’m calm, we’ll see,” he added.
Milos Zeman said he had said all he wanted to say.
“Now it’s the turn of citizens,” he added.
Though Czechs are generally disillusioned with politics, they have been turning out in droves to chose the two very different candidates – Milos Zeman, the acerbic former Social Democrat prime minister, and Karel Schwarzenberg, the elderly, aristocratic foreign minister.
Milos Zeman is a hard-drinking, chain-smoking politician, known for his witty put-downs of his political opponents while Karel Schwarzenberg is a titled prince, 75 years of age but wildly popularly amongst young, urban voters, our correspondent says.
In the early 1990s, Karel Schwarzenberg worked as chancellor to the President Vaclav Havel, the leader of the Velvet Revolution that brought down Communist rule in 1989.
The vote is the first time the president is being directly elected by the public.
The new president will represent the Czech Republic abroad and appoint candidates to the constitutional court and the central bank, but does not carry much day-to-day power.
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