The investigation, launched on the antitrust authority's own initiative, will decide whether AB InBev has used its "dominant" role on the Belgian drinks market to hinder imports of its beer from neighbouring countries, such as the Netherlands and France.
"AB InBev's strong position on the Belgian beer market is not a problem," EU Competition Commissioner Margrethe Vestager said in a statement today.
"However, we want to make sure that there are no anticompetitive obstacles to trade in beer within the European Single Market. Keeping out cheaper imports of its beer from neighbouring countries would be both against the interests of consumers and anti-competitive."
The commission's initial concerns are that the world's largest brewer is pursuing a "deliberate strategy" to restrict the so-called "parallel trade" of its beer to its home market.
It may have done this by changing the packaging of beer cans and bottles to make it harder to sell them in other countries or by limiting "non-Belgian" retailers' access to rebates and key products to prevent them from bringing less expensive products to Belgium.
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"We confirm that the European Commission has opened investigation proceedings in, in relation to the Netherlands, France and/or Belgium," an AB InBev spokesperson said.
"We are fully cooperating with the European Commission."
The South African competition authority announced today it had cleared the acquisition with conditions.