It will look into claims that IBM unlawfully forces users of its mainframe software to use its hardware, and that it discriminated against other companies which service its machines.
EU competition law controls the behaviour of companies that are dominant in their market more closely than that of other companies. The Commission, which enforces EU competition law, is investigating whether or not IBM abused its dominant position in two ways.
The investigations relate to the market for mainframe computers, which are large, expensive machines at the heart of many corporate data systems.
T3 and Turbo Hercules sell software that emulates the functions of IBM's mainframe operating system software. They lodged complaints with the Commission, claiming that forcing users of the operating systems to use IBM hardware was anti-competitive and an abuse of a dominant position.
"IBM is alleged to have engaged in illegal tying of its mainframe hardware products to its dominant mainframe operating system," said a Commission statement. "The complaints contend that the tying shuts out providers of emulation technology which could enable the users to run critical applications on non-IBM hardware."
Turbo Hercules founder Roger Bowler said that he "welcomed" the Commission's investigation.
"Hopefully, it will lead to remedies that will allow companies like TurboHercules to compete in the mainframe market," he said. "We simply ask that customers be allowed to run their mainframe applications on the hardware of their choice."
Hercules is a piece of open source software that emulates IBM mainframes. Turbo Hercules is a company which sells a platform on which organisations can run mainframe software.
The company said that Hercules is useful for students or software developers who want to gain experience of mainframe systems without potentially damaging major systems, and for organisations that want to run mainframe systems at a relatively low cost.
The European Commission will also investigate IBM's treatment of companies which compete with it in the market to service mainframes. That part of the investigation was not prompted by a complaint but by the Commission's own views.
"The Commission has concerns that IBM may have engaged in anti-competitive practices with a view to foreclosing the market for maintenance services (i.e. keeping potential competitors out of the market), in particular by restricting or delaying access to spare parts for which IBM is the only source," said the Commission statement.
The Commission said that it would investigate the two issues "as a matter of priority".