A method and apparatus for scrambling and descrambling data in a computer system includes transmitting non-scrambled data from a first high speed inter chip (IP) link circuit located on a first chip to a first serializer/deserializer (SERDES) physical (PHY) circuit located on the first chip, the first high speed link IP indicating the data is not scrambled. The received non-scrambled data is scrambled by the first SERDES PHY circuit and transmitted to a second chip. The received scrambled data is descrambled by a second SERDES PHY circuit located on the second chip. The non-scrambled data is transmitted by the second SERDES PHY circuit to a second high speed link IP circuit located on the second chip to a third circuit for further processing or transmission.