CTE stands for chronic traumatic encephalopathy. It's is a degenerative brain disease linked to head trauma suffered by football players. Samples of brain tissue from 165 former football players (either pro, semi-pro, or college) were studied by researchers at the Veteran's Administration and Boston University; CTE was found in 131 of those samples. Forty percent of the players who had it were linemen, meaning that the disease is likely caused by repeated smaller collisions, not by the more violent but rarer collisions which cause concussions (1).
Of course, it's not just football players who can get CTE. Anyone who sustains regular blows to the head can develop it. For example, researchers have followed the disease in boxers since the 1920s. It's not always obvious what the original cause of the trauma was, since the damage may not become apparent for years or even decades after the end of active involvement in sports (2).
These images compare the brain of a healthy adult with a brain from someone who suffers from CTE.
By Boston University Center for the Study of Traumatic Encephalopathy [CC BY-SA 4.0 (http://creativecommons.org/licenses/by-sa/4.0)], via Wikimedia Commons