The germ theory of disease is the currently accepted scientific theory for many diseases. It states that microorganisms known as pathogens or "germs" can cause disease. These small organisms, too small to be seen without magnification, invade humans, other animals, and other living hosts. Their growth and reproduction within their hosts can cause disease. "Germ" refers to not just a bacterium but to any type of microorganism, such as protists or fungi, or other pathogens that can cause disease, such as viruses, prions, or viroids. Diseases caused by pathogens are called infectious diseases. Even when a pathogen is the principal cause of a disease, environmental and hereditary factors often influence the severity of the disease, and whether a potential host individual becomes infected when exposed to the pathogen. Pathogens are disease-carrying agents that can pass from one individual to another, both in humans and animals. Infectious diseases are caused by biological agents such as pathogenic microorganisms as well as parasites.

A scientific theory is an explanation of an aspect of the natural world and universe that can be repeatedly tested and corroborated in accordance with the scientific method, using accepted protocols of observation, measurement, and evaluation of results. Where possible, some theories are tested under controlled conditions in an experiment. In circumstances not amenable to experimental testing, theories are evaluated through principles of abductive reasoning. Established scientific theories have withstood rigorous scrutiny and embody scientific knowledge.