Yes, it is pretty well established that cortisol causes the hippocampus to shrink [1]. Studies also show that the hippocampus shrinkage in PTSD is reversible with treatment [2].

That is just one example, but there are quite a lot of other long-term structural changes in the brain after chronic stress.

[1] http://www.biologicalpsychiatryjournal.com/article/S0006-322... [2] http://www.biologicalpsychiatryjournal.com/article/0006-3223...