The germ theory was proposed by Louis Pasteur in 1857. The germ theory states that microscopic particles cause certain diseases. His germ theory led to several advances in understanding disease. 

Today we know that disease causing agents are called pathogens, and that pathogens can be a variety of organisms (or non-living things) of various shapes and sizes. 

Let's just take a look at a few to begin with.

Bacteria, single-celled organisms can cause illness by destroying cells or releasing toxins. Viruses can also cause disease when infecting a cell, and causing the host cell to produce more viruses. Fungi can be found as multicellular or single-celled and usually occur in warm and damp places. Protozoa which are single-celled organisms use host cells to complete their life cycles and take nutrients from the host cell. Parasites are multicellular organisms that grow and feed on a host, sometimes killing the host. 

The table below gives some common infections diseases and the pathogen that causes that disease.

Type of Pathogen Disease How it Spreads
virus HIV body fluids
bacteria Pneumonia airborne
protozoa Malaria mosquito bite