In biology, a pathogen (Greek: πάθος, pathos "suffering", "passion" and -γενής, -genēs "producer of"), in the oldest and broadest sense, is any organism, agent or micro-organism that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a germ.

The term pathogen came into use in the 1880s. Typically, the term pathogen is used to describe an infectious microorganism or agent, such as a virus, bacterium, protozoan, prion, viroid, or fungus. Small animals, such as helminths and insects, can also cause or transmit disease. However, these animals are usually referred to as parasites rather than pathogens. The scientific study of microscopic organisms, including microscopic pathogenic organisms, is called microbiology, while parasitology refers to the scientific study of parasites and the organisms that host them.

There are several pathways through which pathogens can invade a host. The principal pathways have different episodic time frames, but soil has the longest or most persistent potential for harboring a pathogen.

Diseases in humans that are caused by infectious agents are known as pathogenic diseases. Not all diseases are caused by pathogens, such as black lung from exposure to the pollutant coal dust, genetic disorders like sickle cell disease, and autoimmune diseases like lupus.