Once your character begins to explore the Caverns of Chaos deeper than D: 9 (and most other dungeons with DL 10 or higher levels), he/she will slowly start becoming corrupted by the essence of chaos, due to his/her proximity to the Chaos Gate. Once every few turns (higher frequency at lower levels), the PC gains 1 corruption point (adjusted by Appearance and other factors). At D:45 and deeper in the CoC, the PC instead gains 3 corruption points at a time. Background corruption increases by 1 point every 100 days (+1 after 100 days, +2 after 200 days, +3 after 300 days), resetting back to normal at the start of a new year.
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Generally, background corruption will not be a big issue until the end of the game, where you may pick up several unwanted corruptions. At this point, it may be worthwhile to consider doing the Unicorn quest, which will remove all corruption, once.
How to minimize background corruption Edit
Obviously, spend as little time as possible in the deeper levels (45+) of the CoC. Don't perform turn-intensive activities such as smithing or fletching in corrupting areas such as Darkforge.
Use magic mapping and teleportation to quickly locate and ascend/descend the stairs. If you explore the level — to clear out a greater vault, perhaps — don't spend lots of time going back and forth from one long corridor to another. Use teleportation or digging to quickly arrive at your destination. Obviously, digging up a level with a pick axe is another bad idea, unless you've got a very high Mining skill. Monks can kick walls to rubble, Wizards can cast Mystic Shovel, and other classes can use a wand of digging. Some areas don't allow teleportation; in this case, you'll just have to take the long way.
Use blessed seven league boots to minimize the amount of game time that passes during wilderness treks. In addition, some skills and class powers can reduce the cost of walking in the wilderness. Rangers and Druids specialize in this. If you don't have any way of doing this, stay out of forests, hills, and mountains as much as possible.
Plan ahead when you go to the wilderness. Since you'll need to at the very least get the Chaos Orb of Elemental Fire, and most likely will also want to obtain the ring of the High Kings and free the spirit of Griff Bloodax in the Dwarven Graveyard in order to delve deeper into the CoC, you might as well get them all done at once, instead of backtracking constantly. If you haven't done so already, this would also be a great time to raid Darkforge. Try to choose the most efficient route (i.e. the one which involves walking the least tiles) when travelling.
Closing the Chaos Gate removes almost all background corruption from the game, with the exceptions of the Scintillating Cave and the SIL, allowing corruption-free exploration of remaining game areas. In practice, this is of limited value since the PC has already won by this point. It is occasionally useful to do this on D: 50 if the PC is in desperate need of health or PP regeneration between battles with the balors.