Fernando Poe Jr. 2004 presidential campaign

One of the primary issues that Poe faced during the campaign period were three disqualification cases filed before the Commission on Elections (Comelec) by attorneys Maria Jeanette C. Tecson, Zoilo Antonio Velez and Victorino X. Fornier. These cases were subsequently consolidated and elevated to the Supreme Court.[4] Even though Poe was born in the Philippines, the lawyers who filed the disqualification cases argued that he was not a natural-born Filipino, a requirement for a presidential candidate. They argued that he was an illegitimate child who should have followed the citizenship of his American mother. They further argued that Poe's father was not a Filipino because records indicated that Poe's father was a Spanish national. The Supreme Court voted 8–5, with one abstention, in favor of Poe. The high court upheld the previous Comelec ruling and declared Poe was a "natural-born citizen and qualified to run".[5] Supreme Court Justice Hilario Davide Jr. said a preponderance of evidence established that Poe's father was a Filipino because Poe's grandfather, Lorenzo, had not declared allegiance to Spain by virtue of the Treaty of Paris and the Philippine Bill of 1902.[5] Davide said that, in the case of an illegitimate child whose father is a Filipino and whose mother is an alien, proof of paternity is enough for the child to take after the citizenship of his putative father.

Arroyo, taking her oath of office for a full-term as President in Cebu City. In front of her is Chief Justice Hilario Davide Jr. The result of the election was a loss for Poe.

Political critics charged Poe of being heavily linked to political interest groups, and tried to compare his candidacy to that of Estrada, who ran on a similar platform, but was deposed from office and put under house arrest after numerous corruption scandals. While initially seen as the frontrunner in the campaign, his performance in opinion polls was eventually surpassed by the incumbent Gloria Macapagal Arroyo, who did win the election.[7] The poll protest was later thrown out by the Supreme Court acting as the Presidential Electoral Tribunal[8] There is a controversy, known as the Hello Garci scandal, on whether Gloria Macapagal Arroyo had actually won the elections due to allegations of vote rigging, but this was denied by Arroyo.

After Poe's unsuccessful bid to the presidency, his supporters, which include the deposed Estrada's supporters, viewed the election results as flawed, and came under legal protest by Poe and his vice-presidential running-mate, former Senator Loren Legarda.[9] The poll protest was later thrown out by the Supreme Court acting as the Presidential Electoral Tribunal,[8] as well as Legarda's protest.[10]