At least 27 people were killed just before polls opened across the archipelago, where thousands of powerful local posts are also up for grabs. Bombs exploded in several rural areas.
"I am praying for peace and unity in our country," Arroyo said after voting on a steamy tropical morning in her home province of Pampanga near Manila.
Opinion polls indicate that Arroyo, a close ally in the US-led's so-called war on terror, beating action movie hero Fernando Poe Jr by seven percentage points. Three other contestants have scant chance.
Arroyo, 57, a US-trained economist and daughter of a former president, has the support of big business, charismatic Christian groups and much of the political elite.
Poe, 64, who left school at 15, inherited the poor supporters of deposed president Joseph Estrada. He was also backed by Imelda Marcos - the widow of dictator Ferdinand Marcos whose two-decade rule ended in 1986 in the first of two "People Power" uprisings.
Cheating, a 12% bloc of undecided voters and security threats make the outcome far from certain in this mostly Roman Catholic nation of 82 million people.
About 230,000 soldiers and police are on red alert after warnings of attacks by Muslim separatists, even though feuds between candidates and clashes with communist rebels caused most of the 100 deaths during the 90-day campaign.
Police said they killed seven armed men from an unidentified political group in a northern province on Sunday, while a campaign aide was shot dead on Monday in central Cebu.
Opinion polls predict a win for
Gloria Arroyo (R)
Six people were killed in ambushes in Mindanao, where several Muslim groups are fighting for an Islamic state.
Poe, in a pink shirt and his trademark dark glasses, was
mobbed by supporters as he voted at a Manila school.
"Peace to all," the strong, silent and gun-toting star of 282 films said in a typically brief statement.
Television exit surveys will give a preliminary picture after the polls close at 3:00 pm (07:00 GMT). The official results will take a month, although a count by an independent watchdog should give an accurate prediction within a week.
Nearly two decades after the protests that toppled Marcos, the nation faces widespread corruption and debts that eat up a third of state spending, leaving little to lift about 30 million people out of crushing poverty.
Results are expected at 07:00GMT
"Few Filipinos are expecting dramatic change in their lives," the Philippine Star newspaper said in an editorial. "The same families and political groupings dominate the political firmament, backed by the same moneyed supporters."
Voters will also elect a vice president, 12 senators, 200 members of the House of Representatives and 17,000 posts such as governor and town mayor.
Arroyo, who survived a brief military mutiny in July, rose to president three years ago after huge anti-graft protests ended the turbulent term of Poe's friend Estrada, a former film star.
Poe apparently failed to parlay his fame into votes on the same scale as Estrada did when he swept to a landslide victory in 1998. Poe's silences on policy have rattled markets nervous about a heavy dependence on foreign debt.