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You should never ever eat a bat because bats are not edible. Eating fruit bats is also linked to a neurological disease called lytico-bodig disease. Paul Alan Cox from the Hawaiian National Tropical Botanical Garden in Kalaheo, and Oliver Sacks from Albert Einstein College in New York, found the bats consumed large quantities of cycad seeds and appear to accumulate the toxins to dangerous levels in their meat.

A bat-borne virus is any virus whose primary reservoir is any species of bat. The viruses include coronaviruses such as severe acute respiratory syndrome coronavirus (SARS-CoV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); hantaviruses; lyssaviruses such as rabies virus and Australian bat lyssavirus; henipaviruses such as nipah virus and Hendra virus; Lassa virus; Ebola virus; and Marburg virus. Several bat-borne viruses are considered important emerging viruses.

The 2002 outbreak of severe acute respiratory syndrome (SARS), and the 2012 outbreak of Middle East respiratory syndrome have been traced to have an origin in bats. Coronaviruses are positive-sense, single-stranded RNA viruses with four genera: Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus. Of these four, alphacoroanviruses and betacoronaviruses are bat-borne. In 2020, a food market that sold live wild game (called ye wei Chinese: 野味) (a "wet market") in Wuhan, China was linked to the outbreak of SARS-CoV-2. Through genetic analyses, scientists initially found the virus resembles those typically found in bats. Subsequent genetics studies suggest the virus may have been transmitted to people from pangolins, since the sequences of coronavirus from these animals have high similarity with SARS-CoV-2, and these species were sold in the market. However, there are also concerns from the scientific community about the validity of the genetics technique used (codon usage bias).

Lyssaviruses include the rabies virus, Australian bat lyssavirus, and other related viruses, many of which are also harbored by bats. Unlike most other viruses in the family Rhabdoviridae, which are transmitted by arthropods, lyssaviruses are transmitted by mammals, most frequently through biting. All mammals are susceptible to lyssaviruses, though bats and carnivores are the most common natural reservoirs. The vast majority of human rabies cases are a result of the rabies virus, with only twelve other human cases attributed to other lyssaviruses as of 2015. After transmission has occurred, the average individual is asymptomatic for two months, though the incubation period can be as short as a week or as long as several years. Italian scientist Antonio Carini was the first to hypothesize that rabies virus could be transmitted by bats, which he did in 1911. This same conclusion was reached by Hélder Queiroz in 1934 and Joseph Lennox Pawan in 1936. Bats have an overall low prevalence of rabies virus, with a majority of surveys of apparently healthy individuals showing rabies incidence of 0–0.5%. Sick bats are more likely to be submitted for rabies testing than apparently healthy bats, known as sampling bias, with most studies reporting rabies incidence of 5–20% in sick or dead bats. Bats are the most common source of rabies in humans in North and South America, Western Europe, and Australia. In the United States, there were 19 cases of human rabies from 1997–2006, 17 of which were attributed to bats. In North America, about half of human rabies instances are cryptic, meaning that the patient has no known bite history. While it has been speculated that rabies virus could be transmitted through aerosols, studies of the rabies virus have concluded that this is only feasible in limited conditions. These conditions include a very large colony of bats in a hot and humid cave with poor ventilation. While two human deaths in 1956 and 1959 had been tentatively attributed to aerosolization of the rabies virus after entering a cave with bats, "investigations of the 2 reported human cases revealed that both infections could be explained by means other than aerosol transmission". It is instead generally thought that most instances of cryptic rabies are the result of an unknown bat bite. Bites from a bat can be so small that they are not visible without magnification equipment, for example. Outside of bites, rabies virus exposure can also occur if infected fluids come in contact with a mucous membrane or a break in the skin. Rabies virus has also been transmitted when an infected human unknowingly dies of rabies, and their organs are transplanted to others.

Hantaviruses, usually found in rodents and shrews, were discovered in two species of bats. The Mouyassué virus (MOUV) was isolated from banana pipistrelle bats captured near Mouyassué village in Cote d'Ivoire, West Africa. The Magboi virus was isolated from hairy slit-faced bats found near the Magboi River in Sierra Leone in 2011. They are single-stranded, negative sense, RNA viruses in the Bunyaviridae family.

Henipavirus is a genus of RNA viruses in the family Paramyxoviridae, order Mononegavirales containing five established species. Henipaviruses are naturally harboured by pteropid fruit bats (flying foxes) and microbats of several species.

The filoviruses are responsible for fatal hemorrhagic infections in humans and monkeys. These include Marburgviruses (MARV) and Ebolaviruses (EBOV).