This year, a new biometric identification system was set up that requires voters to verify their identity and registration using a fingerprint reader that often needs several tries before it works.
Fears of violence were increased by the murder of an electoral official in charge of technology days ahead of the polls.
The Kenyans take these elections seriously as reports say voter queues are longer than ever. More than 14,000 candidates are standing in those elections.
A key concern is whether Kenya will echo its 2013 election, a mostly peaceful affair despite opposition allegations of vote-tampering, or the 2007 election, which led to violence fueled by ethnic divisions that killed more than 1,000 people.
Shrouded in fears of violence, the vote pits President Uhuru Kenyatta, a wealthy 55-year-old businessman and the son of Kenya's founding president, against Raila Odinga, 72, a former political prisoner and son of Kenya's first vice-president. "They had to finish with me before letting someone else in", Tom Bunde, a voter said.More news: Officer shot, killed in Clinton Missouri
Kenya's president and opposition leader both held election rallies outside their ethnic strongholds this week, as the candidates push harder to win votes in areas dominated by their rivals. He claims elections in 2007 and 2013 were stolen from him.
The polls are seen as a litmus test of Kenya's progress since a disputed 2007 election sparked two months of violence which left more than 1,100 people dead and 600,000 displaced.
There were still some problems with the vote, he said: delays, some agents being denied entry to polling stations, names missing from the register, and the failure of some electronic voter identification devices. Twenty one of Kenya's 47 counties have higher numbers of women registered to vote than men, including Turkana, Samburu, two of seven counties considered swing regions in this election, according to the risk consultancy Maplecroft.
A tight race is expected between Kenyatta, who is seeking a second term, and Odinga, a political veteran intent on becoming Kenya's fifth president in his fourth attempt at the top job of the nation.
Thousands of global observers have been monitoring the vote amid fears of a repeat of the violence that plagued the country following elections a decade ago.More news: Israel seeks closure of Al Jazeera offices
In Kenyatta's home town Gatundu, north of Nairobi, a voter who identified herself only as Gathoni also arrived early to "vote for my favourite president", who will himself cast his ballot at the polling station later in the morning.
Nearly 20 million people are registered to cast their votes for a new president as well as members of parliament, senators, governors and local councilors.
Vote counting got underway in several parts of Kenya Tuesday evening following close of polling at the official time: 5pm EAT.
Over 150,000 police officers have been deployed to ensure that the electoral body - the Independent Electoral and Boundaries Commission - conducts the exercise smoothly at 40,883 polling stations across the country.
If no victor is declared, the election will go to a runoff, which would be a first in Kenya's history.More news: Samsung and Anritsu claim 1.2 Gbps with 6 carrier aggregation