Bacteria are microscopic single-celled organisms at least 1 micron long. Most bacteria species are harmless to humans; indeed, many are beneficial (eubacteria). But some are pathogens, including those that cause cholera, diphtheria, leprosy, plague, pneumonia, strep throat, tetanus, tuberculosis, and typhoid fever.

Viruses are tens or hundreds of times smaller than bacteria. They are not cellular, but consist of a core of genetic material surrounded by a protective coat of protein. Viruses are able to survive and reproduce only in the living cells of a host. Once a virus invades a living cell, it directs the cell to make new virus particles. These new viruses are released into the surrounding tissues, and seek out new cells to infect. The roll call of human diseases caused by viruses includes mumps, measles, influenza, rabies, hepatitis, poliomyelitis, smallpox, AIDS, and certain types of cancer.

Fungi are a varied group of generally small organisms that get their food from living or dead organic matter. They germinate from reproductive cells called spores, which often have a thick, resistant outer coat that protects against unfavorable environmental conditions. This enables spores to survive for long periods of time, which adds to the difficulty of treating fungal infections. Some fungi are external parasites of humans, causing skin conditions such as ringworm, athlete's foot, and jock itch. Other fungi invade internal tissues; examples include yeast that infect the genital tract and several fungi species that cause a type of pneumonia.

Protozoans are single-celled, animal-like organisms that live in moist environments. Perhaps the most infamous pathogenic protozoans are species of the genus Plasmodium, which cause malaria, an infectious disease responsible for over 2 million deaths worldwide each year. Members of the genus Trypanosoma produce trypanosomiasis, also known as African sleeping sickness, and Chagas' disease. Other protozoans cause giardiasis, leishmaniasis, and toxoplasmosis.

Parasitic flatworms include tapeworms, which live in the intestines of a host organism. They have a ribbon-like body that may be up to 9 m (30 ft) in length, depending on the species. Hooks and suckers on the head attach a tapeworm to the intestinal wall, and a tough outer coating protects against the host's digestive juices. Another group of parasitic flatworms is flukes, which are responsible for several serious tropical diseases, most notably schistosomiasis.

Roundworms, or nematodes, are small, tubelike worms that are pointed at both ends. Species that infect human intestines include pinworms, hookworms, threadworms, and members of the genus Ascaris. Trichinella spiralis can invade human muscle tissue, often from eating infected pork that has been improperly prepared, causing a disease called trichinosis.

Prions are extremely tiny protein particles found in the brain, nerve, and muscle cells. A controversial theory states that prions cause disease by changing normal proteins into an abnormal shape. These mutated proteins in turn force other proteins to change shape, leading to destruction of tissue, primarily in the brain. Some researchers have hypothesized that prions cause transmissible spongiform encephalopathies, a group of rare infectious diseases that includes Creutzfeldt-Jakob disease in humans, scrapie in sheep, and bovine spongiform encephalopathy (commonly known as mad cow disease) in cattle. Some evidence suggests that prion-related disease can be transmitted through food infected with mutated proteins.