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I am working on a project that requires that I transmit USB 2.0 over 0.1' headers due to an old design of a test board that used to use low speed USB.

The 0.1' headers are an unshielded and I worry that EMI will cause interference to other sections of the system. Is there anything else I can do to remove radiated noise other than wrapping the connection in foil? Is there a termination scheme or any other techniques to deal with unwanted effects/coupling from the exposed high-speed lines that would help?

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Are you running USB 2.0 at full or high speed? Is this USB interface internal you your system or does it need to pass USB compliance testing?

I'm guessing you can't add any gnds to your cable or connector on either side? If you could that's definitely something to try.

Short of that you could try some series resistors, or series ferrites or even small caps in parallel. All of that will slow your edge rate down or reduce the amount of high frequency content of your signal. Of course that will close your eye a bit too and may violate spec.

Finally maybe a common mode choke like this one made for USB 2.0. That will take out any common mode component.

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