Polls began at 7:00 a.m. local time (13:00 GMT), although queues outside the polling stations were visible at least an hour in advance, the local Radio Sonora es la Noticia said.
Former President Perez Molina resigned earlier this week and was arrested on accusations of accepting bribes from businesses that wanted to avoid paying import duties.
Guatemalan authorities expect the ongoing probe to affect the voter turnout, according to the TeleSur television network. If none of the candidates clears the 50-percent threshold there will be a run-off in October.
There have been calls for Guatemalans to spoil ballots and wear black to polling stations in a protest against the corrupt government, the BBC said Sunday.