Supporters of secession were jubilant.
"Today is an important day for all of Crimea, Ukraine and Russia," voter Manita Meshchina said in Sevastopol, the Crimean port where Russia now leases a major naval base from Ukraine for $98 million a year.
More than 70 people surged into a polling station in the city within the first 15 minutes of voting Sunday.
"Today is a holiday!" said 66-year-old Vera Sverkunova, breaking into a patriotic war song: "I want to go home to Russia. It's been so long since I've seen my mama."
A vote backing secession not only would leave Russia facing strong sanctions by the West but could encourage the pro-Russian sentiment that is rising in Ukraine's east and lead to further divisions in this nation of 46 million. Western Ukraine and the capital of Kiev are strongly pro-West and Ukrainian nationalist.
The referendum comes two weeks after Russian-led forces seized control of Crimea. Locals say they fear oppression by the new Ukrainian government that took over when President Viktor Yanukovych fled to Russia last month.
"It's like they're crazy Texans in western Ukraine. Imagine if the Texans suddenly took over power [in Washington] and told everyone they should speak Texan," said Ilya Khlebanov, a voter in the Crimean capital of Simferopol.
Ukraine's new prime minister insisted again Sunday that neither Ukraine nor the West will recognize the referendum, which he said was conducted at gunpoint.
"Now, on the territory of the autonomous republic of Crimea under the stage direction of the Russian Federation, a circus performance is underway: the so-called referendum," Prime Minister Arseniy Yatsenyuk told a government meeting. "Also taking part in the performance are 21,000 Russian troops, who with their guns are trying to prove the legality of the referendum."
As soon as the polls closed, the White House once again denounced the vote.
"The international community will not recognize the results of a poll administered under threats of violence," it said in a statement. "Russia's actions are dangerous and destabilizing."
Russia raised the stakes Saturday when its forces, backed by helicopter gunships and armored vehicles, took control of the Ukrainian village of Strilkove and a key natural gas distribution plant nearby -- the first Russian military move into Ukraine beyond the Crimean peninsula of 2 million people. The Russian forces later returned the village but kept control of the gas plant.
On Sunday, Ukrainian soldiers were digging trenches and erecting barricades between the village and the gas plant.
"We will not let them advance further into Ukrainian territory," said Serhiy Kuz, commander of a Ukrainian paratrooper battalion.