Libyans have been voting in their first free national election for 60 years.
They are selecting a temporary assembly which will have the task of picking a cabinet and a prime minister.
Voting began late in some cities where gunmen disrupted voting, and one person was killed in a shooting close to a polling station in Ajdabiya.
Nevertheless, overall turnout has been described as high, with voters choosing their first government since Col Gaddafi came to power in 1969.
Few Libyans remember their last national vote in 1965, when no political parties were allowed.
Even fewer took part in their country's first parliamentary elections in February 1952, shortly after independence.
'Free at last'
Polls opened at 08:00 (06:00 GMT), with reports of queues forming outside polling stations in the capital Tripoli.
"I feel free at last. It's a feeling I cannot describe: Like a human being," Asmaddin Arifi told the BBC.
Many voters carried the black, red and green flag of the Libyan revolution as they went to the polls.
Armed men stopped voters casting their ballots in the port town of Ras Lanuf. Voting was also disrupted in Brega and Ajdabiya.
Details of the fatal shooting in Ajdabiya were unclear but Deputy Interior Minister Omar al-Khadrawi told reporters in Tripoli that it took place as three men in a car tried to "threaten the voting process", Reuters news agency reported.
The head of the election commission Nuri al-Abbar said that 94% of polling stations across the country had opened normally.
Officials said later that voting had taken place in all of Libya's electoral districts and that voting hours were being extended to allow everyone to cast their ballots.
UN Libya envoy Ian Martin said the disruption in the east was unlikely to undermine the credibility of the election.
Many people in eastern Libya are concerned that the oil-rich area will be under-represented in the assembly and marginalised as it was during Muammar Gaddafi's 42-year rule.
The region has been allotted only 60 seats in the 200-seat assembly, while the west will have 100 seats and the south 40, under the system devised by the outgoing National Transitional Council (NTC).
Election officials acknowledged that the election was imperfect but insisted it was crucial for the vote to go ahead.
"It's important for the stability of the country," Salim Ben Tahir from the National Election Commission told the BBC.
"We can do it better in the future but the NTC and the current government are losing legitimacy. People aren't respecting them any more and things are getting out of hand."
Some former rebels have tried to derail the vote by targeting the oil industry, large parts of which are located in the east.
They have shut down several oil terminals, including those at Brega, Ras Lanouf and Sidra, and a significant part of Libya's oil exporting capacity has been disrupted.
In an attempt to defuse the situation, the NTC has said the new parliament will no longer be responsible for naming the panel that will draft Libya's new constitution.
The 60-member committee will be elected in a separate vote at a later date.
Around 2.9 million people are eligible to vote for the 2,600 candidates standing for the new General National Congress, less than a year after Col Gaddafi was toppled after an eight-month uprising.
There are countless political parties taking part in the election but the biggest to emerge so far is the Justice and Construction Party, made up mostly of Muslim Brotherhood members.