With the ruling military council reasserting its control over the legislative process by moving to formally dissolve the recently-elected Parliament in line with a court order, there was much uncertainty around the political future of the country.
Moreover, the powers of the president remain undefined in the absence of a constitution and a parliament, which has been dissolved under controversial circumstances.
The Egyptians are choosing between Muslim Brotherhood candidate Mohammed Morsi, and the deposed president Hosni Mubarak's last prime minister Ahmed Shafiq, a choice not many are happy with.
Polls opened early in the day, and will be open till tomorrow evening, in a run-off that comes after a deeply polarising first round that saw a close fight between Morsi, Shafiq and the Leftist candidate Hamdeen Shabahi.
While Morsi and Shafiq made it to round two, the choice has left the country's revolutionaries who were at the forefront of the anti-Mubarak movement in quite a despair.
While Morsi has tried to portray himself as the candidate of the revolution, Shafiq, who arouses deep feelings of hatred in a section of the population, has promised to bring back the stability of Mubarak's time to a country growing weary of protest.
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However, the fact that the run-off has come days after a shocking Supreme Court ruling that declared the parliament election unconstitutional on certain grounds, has lent fresh uncertainty to the country's politics.
The Supreme Council of the Armed Forces (SCAF) formally moved to dissolve parliament yesterday, and told MPs they were not allowed to re-enter the building, Al Jazeera said. (MORE)