After a day marked by euphoric lines of voters -- and a rock star welcome for Suu Kyi as she voted -- the count began after polling stations shut at 4pm local time (0930 GMT).
Early indications were of an "80 percent" turnout, according to Union Election Commission deputy director Thant Zin Aung -- a figure the opposition will hope favours their bid for a majority.
More than 30 million people were eligible to vote in Myanmar's freest election for a generation.
Her National League for Democracy (NLD) party believes a fair vote will power it into government after a decades-long struggle against army dictatorship.
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But the Nobel Laureate is barred from the presidency by the army-scripted constitution and the NLD faces an uphill struggle as a quarter of seats are still reserved for the military.
In the capital Naypyidaw, President Thein Sein, a one-time top-ranking junta general, smiled for the cameras and held up his little finger, stained with purple ink, after voting.
Many voters remain nervous about how the powerful army will react if it loses with concerns over fraud which riddled previous elections.
But after casting his vote in the capital, Myanmar's powerful army chief said his troops would respect the voice of the electorate.
"Just as the winner accepts the result, so should the loser," Min Aung Hlaing told reporters.
State television later carried a live broadcast of the count in several poll stations.
The day belonged to the queues of people, many wearing traditional longyi sarongs, who swarmed to polling stations across the nation.
"I was very excited and so worried that I might do something wrong that my hands were shaking," said fish-seller Kay Khine Soe of the moment she cast her vote.