Identifying Droppings Squirrel droppings are similar in size to jellybeans or raisins and range from 5 to 8 mm in length. They usually get scattered about as the rodents run and easily blend in with the soil due to their light brown coloration. As tree-dwelling creatures, squirrels often use hollow crevices in tree trunks as toilets. Droppings are generally pill-shaped and cylindrical in appearance, sometimes with tapered ends. Proper Sanitation Individuals attempting to clean squirrel droppings must take precautions so as not to contract diseases such as typhus, leptospirosis, and tularemia. Wearing rubber gloves and face masks in infested areas helps reduce the possibility of breathing in fecal matter or urine. However, until squirrel infestations are eradicated, attempts to clean up are ineffective. Droppings will continue to accumulate so long as the animals are present. Therefore, contacting pest control professionals is the best way to handle both squirrel infestations and the disinfection of surrounding areas.