#1 is rabies. Seriously. Although 1% of bats are believed to carry rabies, 4-6% of wildlife control-captured bats test positive because they are generally not caught easily if they are healthy.
Second to that are the diseases associated with their guano... or droppings. Bat poop, though rich in nitrogen, is also rich in very dangerous diseases.
Histoplasmosis is caused by a fungus (Histoplasma capsulatum). Both humans and animals can be affected. The disease is transmitted to humans by airborne fungus spores from soil contaminated by pigeon and starling droppings (as well as from the droppings of other birds and bats). The soil under a roost usually has to have been enriched by droppings for two years or more for the disease organism to reach significant levels. Although almost always associated with soil, the fungus has been found in droppings (particularly from bats) alone, such as in an attic.
Infection occurs when spores, carried by the air are inhaled — especially after a roost has been disturbed. Most infections are mild and produce either no symptoms or a minor influenza- like illness. On occasion, the disease can cause high fever, blood abnormalities, pneumonia and even death. In some areas, up to 80 percent of the population show evidence of previous infection.
The National Institutes of Health (NIH) has reported a potentially blinding eye condition — presumed ocular histoplasmosis syndrome (OHS) — that probably results from the fungus. NIH estimates that 4 percent of those exposed to the disease are at risk of developing OHS.
Take this seriously.
The current ACIP Recommendations for Human Rabies Prevention— United States, (2008) describes a bat exposure as either direct contact with a bat, or “finding a bat in the same room as a person who might be unaware that a bite or direct contact had occurred (e.g., a deeply sleeping person awakens to find a bat in the room or an adult witnesses a bat in the room with a previously unattended child, mentally disabled person, or intoxicated person).
Human contact may happen between you and a bat if it is in your house, wether you know it or not.
Taken from Michigan DNR's website
The hoary bat is Michigan’s largest with a wingspan of up to 15 inches. Heavily furred, the hoary's dark-colored hair is tipped with white giving it a frosted appearance. Its ears are short and rounded. It’s rarely encountered by people and migrate south in winter. It is a solitary species that spends its summer months in forest trees near water throughout Michigan. Researchers know little about their feeding habits and predators.
The red bat is a solitary bat of forests near water. Its long, pointed wings may stretch 12 inches, and it has short, rounded ears, and a furred tail. Color varies from a bright orange to a yellow-brown, and the males are usually brighter in color than the females. Like most other bat species, the red breeds in fall, but conception is delayed until spring when the female gives birth to one to four pups after a gestation period of 80 to 90 days. Blue jays prey heavily on the offspring. Other predators include opossums, sharp-shinned hawks, great-horned owls, and feral house cats.
The silver-haired bat lives in forested areas near streams and lakes. Similar in size to the red bat, the silver-haired species is black or dark brown with silver on the tips of its hairs. Considered scarce throughout their statewide range, the silver-haired bat is most easily identified by its slow flight, which is typically low to the ground. A solitary species, females are thought to establish nursing colonies in June and July when they give birth to two young. A southern migrant, the silver-haired is preyed upon by skunks and great-horned owls.
The eastern pipistrelle bat does not migrate as it hibernates in caves or abandoned mines through winter in the western Upper Peninsula where it lives year-round. This bat occupies rock crevices and building ledges during the day, and leaves just before sunset to feed on insects. A tiny bat with a wingspan of 10 inches or less, the pipistrelle is often confused with a large moth. Ranging from a golden brown to reddish brown, the species has few known predators.
The northern long-eared bat until recently was also called the Keen's bat, which is now considered a separate species living in Canada. Very large ears make these bats easy to identify at close range. Similar in size to the silver-haired and red bat, the long-eared is brown in color. Although it typically roosts alone in buildings and under tree bark in the summer, small numbers hibernate together in caves, often with big brown bats. The species also forms small nursing colonies of about 30 bats in a tree hollow or under bark.
The evening bat lives in extreme southern Michigan and is easily confused with the little brown bat except the evening bat has a curved, rounded fleshy protrusion (tragus) on the ear instead of a pointed tragus. Their wings span 10 to 11 inches. The evening bat flies low to the ground and is sometimes seen swarming around caves, which it rarely enters. Young are born in summer in colonies that range from a few individuals to several hundred, and litter size is typically two pups.
The little brown bat is especially abundant throughout the state and is the most seen species. A light brown to dark brown in color, little browns are fairly small in size with a wingspan of 8 1/2 to 11 1/2 inches, small ears, and large feet. In summer, colonies of the species live in hot attics and under shingles and siding; in winter, they hibernate in caves, crevices, houses, hollow trees, or mines. Females form nursery colonies away from the males. Little brown bats like to feed on aquatic insects and are frequently seen dipping and diving over water but will also forage over lawns and pastures, among trees, and under street lights.
The big brown bat has a large nose, is reddish to dark brown in color, and sports a wingspan ranging from 12 1/2 to 13 1/2 inches. Its slow, steady flight, and large size make it fairly easy to identify. Beetles, wasps, mosquitoes and flies from pastures, lawns and vacant lots in the city make up its diet. They are late-dusk fliers that often swoop low to the ground. A colonizing species, big browns roost in buildings and under bridges in summer and hibernate in caves, mines, houses, hollow trees, and even storm sewers in winter. Efficient feeders, the species often roosts for a short nap after gorging itself. Porches, garages, and breezeways are good places to find them. The female gives birth to only one pup per year.
The Federally endangered Indiana bat is considered rare in southern Michigan, the only region in the state where it resides. A light brown in color, the Indiana bat closely resembles the little brown bat. A southern migrant, the species forms nursing colonies in tree cavities or under loose bark of trees along forested floodplains.