Edmundo Jacobo, executive secretary of Mexico's Federal Electoral Institute, said that 78,012 ballot boxes of 143,000 will be opened and the votes recounted.
The recount plus the final, official overall count on the presidential vote is expected to be ready by Sunday.
With 99 percent of the vote tallied in the preliminary count, Enrique Pena Nieto of the Institutional Revolutionary Party, or PRI, led with 38 percent of the vote. Andres Manuel Lopez Obrador of the Democratic Revolution Party had 32 percent.
Conservative National Action Party candidate Josefina Vazquez Mota - the first woman candidate for a major party in Mexico - conceded almost immediately, saying none of the exit polls favored her. Her party held the presidency for 12 years after kicking out Pena Nieto's Institutional Revolutionary Party in 2000.
Pena Nieto expressed confidence about the recount, saying, "I trust that the final tally will be consistent with the preliminary count."
Lopez Obrador, the former mayor of Mexico City, said he would not concede defeat until all the votes were counted. Lopez Obrador's narrow loss in Mexico's last election led to charges of voter fraud. This time, election officials insisted elaborate electoral machinery would make fraud almost impossible.
More than 79 million Mexicans were registered to vote in the election.
Pena Nieto, a 45-year-old former governor of the state of Mexico, has promised to crack down on the drug violence that has killed more than 50,000 Mexicans in recent years and create jobs.
The Associated Press contributed to this report.