Many different microorganisms can cause a given condition (for example, pneumonia can be caused by viruses, bacteria, or fungi). It is usually important to know what specific microorganism is causing an illness because the treatment is different for each organism.

There are many ways to identify microorganisms. Taking a sample from the site of infection and examining it under the microscope is often the most rapid method of identifying microorganisms. Sometimes, microorganisms can be recognized by characteristic shapes and colors. However, if the microorganisms are too few or too small to see under the microscope, they may not be found.

Another method of identifying an infectious organism is to grow it in the laboratory so that additional chemical tests can be done. The process of growing the organism is called a culture. Many microorganisms can be grown this way. Cultures can also be used to test the sensitivity of microorganisms to various antibiotics, which can help determine what drug to use to treat an infected animal. This strategy is particularly important because microorganisms are constantly developing resistance to antibiotics that were previously effective.

Some microorganisms are very difficult to culture. These infections can be identified by finding antibodies to the microorganisms in the infected animal's blood or other body fluids. Antibody-based tests are used to identify many infections, but they are not always reliable. Antibodies often stay in the body for many years after an infection has cleared. New tests, such as the polymerase chain reaction, can identify pieces of the genetic material (DNA) of the microorganism, which are present only when the organism is present. These tests are usually performed only when a particular disease is already suspected.