The first dead body was found on Wednesday evening at a time when protesters were trying to head towards the presidential palace where the transition president and members of his government were being held hostage by the presidential guard officers.
On Thursday morning, another young man was shot and killed by the soldiers in Ouagadougou's city-center.
Besides the two bodies, some eyewitnesses said there was a third body that had been seen in a populous suburb of Ouagadougou.
General Gilbert Diendere, a former chief of staff during Compaore's regime, has been declared the leader of the National Council for Democracy which took power after overthrowing the transition government on Thursday.
The soldiers have imposed a curfew from 7:00 p.m. till 6:00 a.m., and have closed the country's aerial and land borders.
Many Burkina Faso towns have been paralysed. Journalists have been prevented from doing their work, while some audiovisual broadcasters have been blocked from broadcasting.
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