Ukraine's new government and most of the international community except Russia have said they will not recognise a result expected to be overwhelmingly in favour of immediate secession.
Some 1.5 million people are called to vote on the diamond-shaped Black Sea peninsula, which is mostly inhabited by ethnic Russians and has been seized by Russian forces over the past month.
AFP reporters saw voters cast their ballots in the regional capital Simferopol, the naval base of Sevastopol and Bakhchysaray -- the hub of the Muslim Tatar community, which is urging a boycott.
"Everyone will vote for Russia," he said.
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Crimea says foreign observers are monitoring the vote but the Organisation for Security and Co-operation in Europe (OSCE) is not because it needs to be invited by national governments.
OSCE military observers aiming to defuse tensions have been prevented from entering Crimea, which is at the centre of the worst East-West confrontation since the fall of the Berlin Wall in 1989.
Voters can choose to become part of Russia or retain more autonomy but stay in Ukraine -- a vote for the status quo is not an option.
Preparations to become part of the Russian Federation -- a process that could take months -- are to begin this week if the people vote for Moscow.