Perks are chosen abilities at the beginning of the game that allow for further customization of your hero, before you even start. These perks show up after your hero is selected, and you are given a choice to choose up to 3 perks in total. Each perk has it's own use and some perks have both pros and cons, while others have no negative bonuses whatsoever. All perks available are the same for each hero.
There does not appear to be any late game perks, so these perks are possibly to help harder difficulties stay on their feet early game.