I have just noticed that one of our servers were connected with 100baseTx instead of 1000baseT. Both end-points support 1000baseT but it was not advertised.

# mii-tool -v eth0
eth0: negotiated 100baseTx-FD, link ok
  product info: vendor 00:50:43, model 11 rev 1
  basic mode: autonegotiation enabled
  basic status: autonegotiation complete, link ok
  capabilities: 1000baseT-FD 100baseTx-FD 100baseTx-HD 10baseT-FD 10baseT-HD
  advertising: 100baseTx-FD 100baseTx-HD 10baseT-FD 10baseT-HD flow-control
  link partner: 1000baseT-FD 100baseTx-FD 100baseTx-HD 10baseT-FD 10baseT-HD

First idea was to check cable. It was the same Cat 5e cable we always use. However, I replaced it with another one of the same type and suddenly Gigabit Ethernet was working again.

# mii-tool eth0
eth0: negotiated 1000baseT-FD flow-control, link ok