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In many cases, the diseases that squirrels can carry and transmit are only diseases that will affect other animals, with cases of squirrel-human diseases being quite rare. There are cases where it can happen, of course, such as with leptospirosis or salmonella. That's why it is vitally important that you clean up every shred of evidence that the animal has ever been in your home, including feces.
Urine is sprayed as the animal runs around, much in the same way that rats and mice expel waste. That urine is not only known to potentially carry diseases, but can even signal to other squirrels, using communication methods called pheromones, to let them know that a nice food source is close by, as is a tidy little nesting spot. Leaving squirrel urine where it is will only cause you a bigger problem later on.
A filter vacuum can be used to get rid of the bulk of the feces, but this isn't the entire job. You will need to make sure you clean the area properly once this step has been done. You can’t just clean up the bits you can see — you must clean up the bits that you can't too, and that's what makes this task such a difficult one.
If you have a steam cleaner, you may find that the job will be quicker and simpler when you use it. You can also use various cleaning products to help eradicate all traces, but make sure that you don't mix them. This can have an adverse reaction and can make you quite sick.
Antibacterial and disinfectant cleaning products are a great place to start, and you will want a bucket filled with warm, soapy water, as well as plenty of scrubbing equipment. You can't forget the gloves, and we would also recommend wearing some sort of eye protection, as well as thick rubber gloves. Everything that you used to clean up the mess must be disposed of also, if you can’t disinfect it thoroughly and effectively. A bonfire is advisable to get rid of everything.
Go back to the Squirrel Removal page, or learn tips to do it yourself with my How to Get Rid of Squirrels guide.