The human physiological defense against common pathogens (such as Pneumocystis) is mainly the responsibility of the immune system with help by some of the body's normal flora and fauna. However, if the immune system or "good" microbiota are damaged in any way (such as by chemotherapy, human immunodeficiency virus (HIV), or antibiotics being taken to kill other pathogens), pathogenic bacteria that were being held at bay can proliferate and cause harm to the host. Such cases are called opportunistic infections.
Some pathogens (such as the bacterium Yersinia pestis, which may have caused the Black Plague, the Variola virus, and the malaria protozoa) have been responsible for massive numbers of casualties and have had numerous effects on afflicted groups. Of particular note in modern times is HIV, which is known to have infected several million humans globally, along with the influenza virus. Today, while many medical advances have been made to safeguard against infection by pathogens, through the use of vaccination, antibiotics, and fungicide, pathogens continue to threaten human life. Social advances such as food safety, hygiene, and water treatment have reduced the threat from some pathogens.
Pathogenic viruses are mainly those of the families of: Adenoviridae, Picornaviridae, Herpesviridae, Hepadnaviridae, Flaviviridae, Retroviridae, Orthomyxoviridae, Paramyxoviridae, Papovaviridae, Polyomavirus, Rhabdoviridae, and Togaviridae. Some notable pathogenic viruses cause smallpox, influenza, mumps, measles, chickenpox, ebola, and rubella. Viruses typically range between 20 and 300 nanometers in length. 
Although the vast majority of bacteria are harmless or beneficial to one's body, a few pathogenic bacteria can cause infectious diseases. The most common bacterial disease is tuberculosis, caused by the bacterium Mycobacterium tuberculosis, which affects about 2 million people mostly in sub-Saharan Africa. Pathogenic bacteria contribute to other globally important diseases, such as pneumonia, which can be caused by bacteria such as Streptococcus and Pseudomonas, and foodborne illnesses, which can be caused by bacteria such as Shigella, Campylobacter, and Salmonella. Pathogenic bacteria also cause infections such as tetanus, typhoid fever, diphtheria, syphilis, and Hansen's disease. They typically range between 1 and 5 micrometers in length.
Fungi comprise a eukaryotic kingdom of microbes that are usually saprophytes, but can cause diseases in humans. Life-threatening fungal infections in humans most often occur in immunocompromised patients or vulnerable people with a weakened immune system, although fungi are common problems in the immunocompetent population as the causative agents of skin, nail, or yeast infections. Most antibiotics that function on bacterial pathogens cannot be used to treat fungal infections because fungi and their hosts both have eukaryotic cells. Most clinical fungicides belong to the azole group. The typical fungal spore size is 1-40 micrometers in length.
Some eukaryotic organisms, such as protists and helminths, cause disease. One of the best known diseases caused by protists in the genus Plasmodium is malaria. These can range from 3-200 micrometers in length.
Prions are infectious pathogens that do not contain nucleic acids. Prions are abnormal proteins whose presence causes some diseases such as scrapie, bovine spongiform encephalopathy (mad cow disease), and Creutzfeldt–Jakob disease. The discovery of prion as a new class of pathogen allowed Stanley B. Prusiner to receive the Nobel Prize in Physiology or Medicine in 1997.
Animal pathogens are disease-causing agents of wild and domestic animal species, at times including humans.
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. An example is the malaria parasite, which can spread from a person near death, by hitching a ride to a healthy person on a mosquito that has bitten the diseased person. This is called horizontal transmission 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.
Evolutionary medicine has found that under horizontal transmission, the host population might never develop tolerance to the pathogen.
Transmission of pathogens occurs through many different routes, including airborne, direct or indirect contact, sexual contact, through blood, breast milk, or other body fluids, and through the fecal-oral route. One of the primary pathways by which food or water become contaminated is from the release of untreated sewage into a drinking water supply or onto cropland, with the result that people who eat or drink contaminated sources become infected. In developing countries, most sewage is discharged into the environment or on cropland; even in developed countries, periodic system failures result in sanitary sewer overflows.
- Bacillus anthracis — the causative agent of anthrax in humans and animals
- Clostridium botulinum — releases the most powerful neurotoxin leading to death from botulism
- Mycobacterium tuberculosis — the causative agent of most cases of tuberculosis
- Mycobacterium leprae — the bacterium that causes leprosy (Hansen's disease)
- Yersinia pestis — pneumonic, septicemic, and the notorious bubonic plagues (Black Death)
- Rickettsia prowazekii — the etiologic agent of typhus fever
- Bartonella spp.
- Spanish influenza virus
- Entamoeba histolica virus amoeba or amoebiasis
- Cancer bacteria
- Emerging Pathogens Institute
- List of clinically important bacteria
- Lists of diseases
- List of human diseases associated with infectious pathogens
- List of infectious diseases
- List of parasites of humans
- The prion diseases STANLEY B. PRUSINER, Scientific American
- Encyclopedia of Biological Invasions - Page 510 Daniel Simberloff, Marcel Rejmánek - 2011 "Pathogens, animal Graham J. Hickling University of Tennessee, Knoxville "Animal pathogens are disease-causing agents of wild and domestic animal species, at times including humans. In the context of invasion biology, the term usually .."