How to Clean the Cage
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First, take out your rats and put them in a safe place while you work.  Then take the bottom off the cage (if you have a wire or plastic cage) and discard the bedding.  Wash the bottom thoroughly.  Also take out any toys that need washing and clean them as well.  If your rats have a litter box, make sure to change the litter in that as well.  Wipe down the rest of your cage with a damp cloth or sponge, making sure to wash any of the levels and anywhere else that the rats may have urinated on.  Once everything has been cleaned, refill the pan with bedding and put the cage back together and return your rats to the cage.
Though using antibacterial cleaning products can be a good idea if you are worried about your rats' health, be careful not to overdo it, as the products can be harmful to your rats if they are not fully rinsed off during cleaning.
If you have a larger cage, it can be more difficult to clean.  If it fits in your shower or bathtub, you can rinse it off that way, or allow it to soak in the bathtub of hot water or hot water with bleach added (make sure you rinse it off afterwards if you are using bleach).  While it is in the tub, use an old toothbrush or soft cloth to wipe down all the surfaces.

Other Cleaning Considerations

If you are using a wire barred cage, it is very likely that the area around the cage will need cleaning as well.  Rats can urinate and even defecate right through the bars, ending up on the surrounding floor, walls, and any furniture closeby.  Rat urine does stain carpets if not properly cleaned frequently, so if your rat cage is in a carpeted room you may want to put a waterproof plastic mat underneath it to help protect your floors.  At cage cleaning time, using a spray cleaning product (Fantastic works great) to remove rat urine and feces from the walls and floors around your rat cage and wipe clean with a damp cloth or paper towel.

How Often Should You Clean?
Depending on the size and type of cage you have, your cage should generally be cleaned once every two weeks.  Larger, well ventilated cages can be left longer if you remove the soiled bedding from the corners (rats tend to urinate in the same few places).  Smaller, poorly ventilated cages must be cleaned very often, or the ammonia can build up and hurt your rat's sensitive respiratory system.

Cage Odors
A clean cage with healthy rats in it should have little to no odors.  If you only replace the bedding when you clean the cage, the cage may still have a smell.  Rats can climb on the bars of their cage and urinate on the walls and even the ceilings!  Unless the cage is cleaned thoroughly, there may still be a lingering smell, especially if you have male rats.  If you don't want to do a thorough clean every time, you don't have to, rats are fairly clean and it usually isn't necessary.  But at least every second or third time you replace the bedding you should wash down the entire cage to reduce the rats' urine odors.
There are some commercial products out there that claim to help cut down on cage odors.  Though I have not personally tested any of these, if you are having a problem and are not sure why, it might be a good idea to try them out.
Something else to consider is that if your cage has a plastic bottom and your cage has been in use for a while, the urine and feces odors may have soaked into the porous surface of the plastic.  If the pan still has a smell after being washed thoroughly, this is likely the case.  All that can be done at this point is to replace the bottom pan.
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