Many symptoms of a parasitic infection are similar to other illnesses, making it particularly important to test for parasites for proper diagnosis and treatment. A comprehensive parasite test, using a stool sample analyzed by a laboratory specializing in parasite testing, is the most effective way to diagnose this type of infection. Parasite testing by examination of stool samples may require multiple samples and the use of a lab that specializes in this type of testing. More comprehensive testing, such as a Comprehensive Digestive Stool Analysis with Parasitology is suggested and available from the same stool sample when bacterial imbalances or digestive problems are suspected.

Most of the common parasites are much too small to be seen in stool with the naked eye, so anything visible may simply be undigested food fibers. The only way to be sure is to look at the sample under the microscope, as part of an Ova and Parasite (O&P) exam. Parasites have a characteristic structure, including digestive organs, that fibers do not have.

Antigen tests are used to detect protein structures on parasites. They can even detect the presence of parasite fragments in a stool sample, which has the advantage of allowing detection of a particular parasite even if it is not seen in an O&P examination.

Blood antibody tests may be ordered to determine whether or not someone has been exposed to a parasite in the past (this may indicate a past or a chronic infection but is not used to detect a current infection).

It is important to have a fresh stool sample because any eggs or parasites that are present may break down in unpreserved stool, making them harder to detect.

Sometimes a biopsy of the small intestines is taken, a small amount of tissue that is examined for parasitic infestation.