Since your cat can't talk, it is often necessary to use a diagnosis of exclusion in these cases. Rule out each issue one by one until you're left with the only answer.
The first step here is to have a consultation with your vet. Always assume that your cat has a physical problem as the cause, unless your vet says otherwise.
If your vet has given the all clear, then you're going to have to assume, for the moment, that your litter box problems are behavioral. Let's try to understand our cat's point of view and see if we can think of some behavioral reasons for not using the litter box.
1. Dirty Cat Box - some cats prefer the box to be extremely clean, and others are willing to allow it to be somewhat less so. No matter what, you should clean your litter box at least once per day. You should also change your litter out completely at least every few weeks. Whenever you change the litter, wash the litter box thoroughly. Be sure to wash the lid too if you have a hooded box.
2. Cat Box Odor - if the litter box doesn't smell quite right, your cat may avoid it. You might think that your litter box smells just fine, but your cat may have a different opinion about the subject.
If you didn't clean it well enough, your cat will know. If you used a scented cleaner, or didn't rinse it well enough, it may not smell right to your cat. It's recommended that you use a solution of one part bleach to 30 parts water to help prevent the spread of parasites and recurring infections. Rinse well and dry thoroughly! When you're finished, the box should not smell like cat waste, soap, or bleach.
3. Litter Box Odor - some cats simply prefer the odor of one brand or type of litter over another. Even unscented litters have an odor your cat can detect and may not like. Be prepared to try different types and brands until you find the right one for your cat.
4. Wrong Litter Type - brand aside, your cat may be turned off by the type of cat litter you use. Switching litter types too fast can be an issue. When you switch litters, add 20 percent new litter to 80 percent old, and then increase the amount of new litter over several days.
5. Litter Box Type - the shape, size, and type of box does matter. For example, some cats may like a hooded box, while others prefer the open kind. Perhaps your cat would like higher walls, or a larger box. If you've recently changed litter boxes, this could be causing a problem.
6. How Many Boxes? - another cause of a cat litter box problem relates mainly to multi-cat households. Remember the one plus one rule when selecting how many boxes you'll need. You should have one box for each cat, and one extra box so that there is never any waiting for a box to free up. Cleaning chores are a little easier if you have more boxes since that keeps each box a little cleaner.
7. Poor Location - I've seen boxes in noisy kitchens and laundry rooms. This is usually a mistake. If your cat is not happy with the location of the box, he may stop using it. Always try to keep the box in an area that is low traffic and low noise. In some cases, finding a good spot for the box is difficult, but do your best.
8. Territorial Issues - territorial arguments are common in multi-cat households. Some cats like to sneak up on others when they're using the box and pounce. If your cat is attacked every time he's in the box, he may grow to hate the box. This is where the one plus one rule for multi-cat households is most important.
9. Stress - if your cat is stressed by a recent move, a new addition to the household, or perhaps simply a behavior shift on the part of a family member, this may be at the root of the box issue. Try to think about what might have changed recently in your cat's life, and then try to ease whatever stress she's under.
Cat litter box problems can usually be solved, once you know the cause. The solution doesn't have to mean getting rid of the cat. Your veterinarian needs to first rule out physical causes so you can tackle the behavior side of things. Think like a cat, and you'll be able to solve your box problems.
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