The October census was held to get a clear image on the country's population almost two decades after the war in which some 100,000 people were killed and more than two million fled their homes.
Early results show that Bosnia counts 585,411 less inhabitants compared to when the last census was held in 1991.
"According to preliminary results, we have registered 3,791,622 people in Bosnia... Who live in 1.16 million households," Zdenko Milinovic, head of the state statistics bureau, told reporters.
According to the 1991 census, Bosnia had a population of 4.4 million, including 43.5 per cent Muslims, 31.2 per cent Serbs and 17.4 per cent Croats.
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Today's Bosnia remains deeply divided along ethnic lines, split between two highly autonomous entities -- the Serbs' Republika Srpska and the Muslim-Croat Federation -- linked by weak joint institutions.
Almost 2.4 million people were registered in the Muslim-Croat Federation, and slightly more than 1.3 million in the Republika Srpska.
European countries generally hold a census every 10 years, but in Bosnia, it has been repeatedly postponed due to disagreement between leaders of the three ethnic groups.