After 300 years of Portuguese rule and a quarter-century under Indonesian military occupation, the people of East Timor were finally allowed today to vote on independence. Analysts believe that barring intimidation, they will choose it overwhelmingly.

The threat of violence has hung heavy over the territory, even though a peace agreement was announced Sunday between pro-independence guerrillas, known as Falintil, and heavily armed anti-independence militia groups, which have been supplied with weapons by some elements of the Indonesian military that oppose East Timorese secession.

But in spite of rumors here in the provincial capital that disruptive attacks by militiamen were imminent, thousands of voters were waiting at polling places by the time they opened at 6:30 a.m. Across the territory, half of the more than 450,000 eligible voters had showed up to vote by 10 a.m., a United Nations official said.

Many voters here in Dili said they were frightened but wanted to take advantage of the opportunity to cast their ballots. Maria Gomes, who works for the wife of the Indonesian-appointed governor, said she would vote for independence. "I am very scared to come here, but we are better off making the decision today," she said. She'll likely be out of a job if most people vote as she did, but Gomes said it would be worth it because the East Timorese would be "freeing ourselves."

East Timor, a tiny, impoverished Pacific island backwater, has for two decades been a largely invisible sore spot, the scene of some of the world's most horrific reported human rights abuses. One of the last Portuguese colonies, it became one of the last victims of Cold-War superpower politics when it was invaded from West Timor by Indonesian troops in 1975 -- with a wink and a nod from the United States.

The pretext for the invasion was that communists were about to turn the territory into "another Cuba" in the Pacific. The Vietnam War had just ended, and the United States and its allies in Southeast Asia feared communist-inspired insurgencies would erupt throughout the region.

Over the years, struggle of the East Timorese to free themselves from Indonesia has attracted some high-level support. The United Nations adopted resolutions; Nelson Mandela took it up as a cause; Pope John Paul II came to visit; and two East Timorese activists won the 1996 Nobel Peace Prize for their tireless campaigning against Indonesia's heavy-handed rule.

Finally, with the fall of Indonesian President Suharto in May 1998, the international community saw a new opportunity to resolve the long-running dispute. But Indonesia now fears that if the East Timorese vote for independence, a string of similar secessionist claims could unravel the country, the world's fourth largest.

In one of Dili's poorest neighborhoods, called Becora, an independence stronghold that has been the scene of militia violence, residents armed themselves Sunday after reports of a possible attack by the Aitarak militia. The neighborhood has been on edge since a crowd recently beat a suspected pro-Indonesian militiaman, prompting fears of reprisals.

"We have rocks, sticks and our traditional weapons," said Jose Amara, 21, who was guarding a corner with a group of young men, one of them with a large knife strapped around his chest. "We are not afraid, because all we want is independence. We are willing to die for it."

Amara's friend, Joao Carvalho, 40, said, "All the militia has been doing is trying to scare people. But they are not scared, because they are eager to go vote."

At the Hotel Tropical in the center of town, scores of Aitarak militiamen were gathering outside, some with automatic weapons visible despite a weapons ban agreed to by both sides.

There were few reports of violence as the vote began today. Two houses were reported burned and militiamen fired shots in west Dili, but there were no reports of injuries. However, Ian Martin, head of the U.N. Assistance Mission in East Timor, said many people were too afraid to leave their homes in the western district of Maliana, which was rocked by deadly attacks by anti-independence militias last week.

With the pervasive fear of violence, the main question in the days leading up to the vote was whether intimidation and terror would be enough to counter the East Timorese people's widespread enthusiasm over their first chance to choose how they will be governed.

"The turnout is the key," said one official from the United Nations, which organized the vote. He said he was heartened that last month, despite similar threats, 450,000 people registered to vote in the territory of 800,000. "The determination of people to go out and vote is so great, it's going to be difficult to stop them."

Dili Bishop Carlos Belo, a winner of the Nobel Peace Prize, appealed to East Timorese on Sunday to vote. "At this time, I ask all of you not to be afraid," Belo said in a message read in churches throughout this overwhelmingly Catholic territory. "Brothers and sisters, a lot of people here at this time are very afraid."

U.N. Secretary General Kofi Annan said the East Timorese have "a unique opportunity to settle a long-running dispute by peaceful means. I appeal to all sides to live up to their responsibilities before history by respecting the democratic process."

Indonesian President B.J. Habibie, in a nationwide address, urged the East Timorese to reject independence and vote to remain part of Indonesia, but he pledged to respect the result of the plebiscite.

It was Habibie who in January set the voting process in motion when he jettisoned 24 years of policy and decided to let the people of East Timor choose their fate. But the policy switch was not entirely accepted by Indonesia's powerful military, which fears that losing East Timor could lead to separatist claims across the sprawling archipelago.

International police advisers are to collect the ballot boxes and take them to a counting center in Dili; the result is to be announced by Sept. 7.