The term pathogen came into use in the 1880s. Typically, the term is used to describe an infectious microorganism or agent, such as a virus, bacterium, protozoan, prion, viroid, or fungus. Small animals, such as certain kinds of worms and insect larvae, can also produce disease. However, these animals are usually, in common parlance, referred to as parasites rather than pathogens. The scientific study of microscopic organisms, including microscopic pathogenic organisms, is called microbiology, while the study of disease that may include these pathogens is called pathology. Parasitology, meanwhile, is the scientific study of parasites and the organisms that host them.

It is common to speak of an entire species of bacteria as pathogenic when it is identified as the cause of a disease (cf. Koch's postulates). However, the modern view is that pathogenicity depends on the microbial ecosystem as a whole. A bacterium may participate in opportunistic infections in immunocompromised hosts, acquire virulence factors by plasmid infection, become transferred to a different site within the host, or respond to changes in the overall numbers of other bacteria present. For example, infection of mesenteric lymph glands of mice with Yersinia can clear the way for continuing infection of these sites by Lactobacillus, possibly by a mechanism of "immunological scarring".

Virulence (the tendency of a pathogen to cause damage to a host's fitness) evolves when that pathogen can spread from a diseased host, despite that host being very debilitated. Horizontal transmission occurs between hosts of the same species, in contrast to vertical transmission, which tends to evolve symbiosis (after a period of high morbidity and mortality in the population) by linking the pathogen's evolutionary success to the evolutionary success of the host organism.

Prions are misfolded proteins that can transfer their misfolded state to other normally folded proteins of the same type. They do not contain any DNA or RNA and cannot replicate other than to convert already existing normal proteins to the misfolded state. These abnormally folded proteins are found characteristically in some diseases such as scrapie, bovine spongiform encephalopathy (mad cow disease) and Creutzfeldt¥Jakob disease.

The vast majority of bacteria, which can range between 0.15 to 700 ?M in length, are harmless or beneficial to humans. However, a relatively small list of pathogenic bacteria can cause infectious diseases. Pathogenic bacteria have several ways that they can cause disease. They can either directly affect the cells of their host, produce endotoxins that damage the cells of their host, or cause a strong enough immune response that the host cells are damaged.

Plants can play host to a wide range of pathogen types including viruses, bacteria, fungi, nematodes, and even other plants. Notable plant viruses include the Papaya ringspot virus which has caused millions of dollars of damage to farmers in Hawaii and Southeast Asia, and the Tobacco mosaic virus which caused scientist Martinus Beijerinck to coin the term "virus" in 1898. Bacterial plant pathogens are also a serious problem causing leaf spots, blights, and rots in many plant species. The top two bacterial pathogens for plants are P. syringae and R. solanacearum which cause leaf browning and other issues in potatoes, tomatoes, and bananas.

Much like viral pathogens, infection by certain bacterial pathogens can be prevented via vaccines. Vaccines against bacterial pathogens include the anthrax vaccine and the pneumococcal vaccine. Many other bacterial pathogens lack vaccines as a preventative measure, but infection by these bacteria can often be treated or prevented with antibiotics. Common antibiotics include amoxicillin, ciprofloxacin, and doxycycline. Each antibiotic has different bacteria that it is effective against and has different mechanisms to kill that bacteria. For example, doxycycline inhibits the synthesis of new proteins in both gram-negative and gram-positive bacteria which leads to the death of the affected bacteria.