Mastercard Inc (NYSE:MA) is under investigation by European regulators in connection with its inter-bank fees. The European Commission issued a press release announcing the investigation today saying that it has concerns that some of the company’s fee practices might be “anti-competitive.”

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In the U.S., both Mastercard Inc (NYSE:MA) and Visa Inc (NYSE:V) are now officially allowed to charge a swipe fee in most states. The fee came as part of a settlement between the credit card companies and nine banks in connection with allegations of fixing credit card processing fees.

The new investigation focuses on MasterCard’s fee structures as they relate to cross-border and Internet purchases throughout the European Union. The European Commission notes that over 40 percent of non-cash payments every year in the EU are made using cards. Back in 2007, the EC did prohibit some of Mastercard Inc (NYSE:MA)’s fee practices.

There are three main fee practices the EC is focusing on. It’s looking at inter-bank fees in connection with payments made by cardholders from countries that are not in the European Economic Area. Regulators are comparing those fees with those charged for cross-border transactions within the EEA, which were part of the fee practices prohibited back in 2007.

Regulators are also examining all of MasterCard’s rules that “limit the possibility for a merchant to benefit from better conditions offered by banks established elsewhere in the internal market.” The third area involves rules like the “honor all cards rule,” which requires merchants to take all kinds of Mastercard Inc (NYSE:MA) cards.

In the EC’s view these practices could restrict competition because inter-bank fees are usually passed to merchants and could slow down business done across borders. The commission said by summer, it tends to propose new regulations on inter-bank fees.

The commission also said it is investigating Visa Inc (NYSE:V) for similar fee practices.