A preliminary investigation by the Commission showed that banks worked together to exclude exchanges from the derivatives market.
This was allegedly because they feared involvement by the exchanges would cut into their huge profits from over-the-counter trading.
Some aspects of derivatives trading have been blamed for exacerbating the financial crisis.
The EU's Competition Commissioner Joaquin Almunia said that the banks now had the chance to respond to the detailed accusations.
He said that they could face fines if the charges were confirmed once the investigation had been completed.
"Exchange trading of credit derivatives improves market transparency and stability," he said.
Collusion between banks to prevent this type of trading would be "a serious breach of our competition rules", he said.
Almunia declined to give an estimate of the size of possible fines on the banks but he said the CDS market at the moment was worth about USD 13 trillion.
The collapse of US investment bank Lehman Brothers in 2008 "showed how derivatives trading is able to destabilise the entire financial system," Almunia said.
It said the two exchanges decided to turn to the International Swaps and Derivatives Association (ISDA) and data service provider Markit to obtain the necessary licences but were turned down because the banks had prevented them from doing so.
The 13 European and US banks targeted are: Bank of America Merrill Lynch, Barclays, Bear Stearns, BNP Paribas, Citigroup, Credit Suisse, Deutsche Bank, Goldman Sachs, HSBC, JP Morgan, Morgan Stanley, Royal Bank of Scotland and UBS.
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