Each serial lane must be synchronized to align the frames between the transmitter and the receiver and to synchronize the reception scrambler with the transmission scrambler.

The synchronization is controlled through the synchronization (SYNC) signal sent to the receiver and to the transmitter.

The receiver must receive the SYNC signal prior to receive the ESIstream Synchronization Sequence (ESS).

The transmitter generates the ESS when receiving the SYNC signal. The length of the SYNC pulse should be at least as long as one ESIstream frame period (16-bit). ​

When it is received by the transmitter, it will send an alignment pattern which is 32 frames alternating between 0xFF00 and 0x00FF. The sequence bypasses the scrambling and disparity processing (the sequence is DC balanced). This alignment pattern is used by the receiver to align its data on the transmitter output data.

After these 32 frames, the transmitter starts sending 32 additional frames containing the scrambling PRBS alone. These frames contain 14 bits of the PRBS plus the clk bit and the disparity bit. They go through the disparity processing, as the PRBS value will start to impact the running disparity of the transmission.

The receiver will detect the transition from the alignment pattern to the PRBS alone. The PRBS is reset by the transmitter when receiving the SYNC to avoid the first frame of the PRBS initialization being either 0x00FF or 0xFF00; this to ensure that passive detection is precise to the frame.

The receiver will determine its PRBS initial value after receiving 2 valid frames of PRBS Alignment Sequence. These 2 frames contain 28 bits of the PRBS sequence; the receiver needs 17 bits to determine its PRBS initial value. After that, the synchronization of the link is complete. ​