We recently encountered a chimney that had been occupied by a raccoon for some time. We were unable to clean this chimney because of the chance that the raccoon had left droppings in this chimney. These droppings can contain a particularly unpleasant parasitic roundworm that can cause life-threatening symptoms if they are ingested.

See this CDC paper for more information

Removing these droppings and sterilizing the infected areas requires specialized equipment and training which we do not have. In order to have them removed, you will likely spend a fair some of time and money, this can be prevented by having some sort of rain cap on your chimney. These can be ordered in a variety of sizes and styles from many websites, purchased from local hardware stores like Lowes or Home Depot, or, we can supply and install them for a fee.