As viewed under a microscope, a the cuticle or body covering of a typical plant-parasitic nematode is transparent allowing the viewing of internal systems. The major organs visible are various components of the digestive system and of the reproductive system.

At the anterior end, all plant parasitic nematodes have a stylet (also called a spear), which can be protruded and used to penetrate plant cells like a hypodermic needle. Nematodes which feed on fungi and other sources of food can also possess stylets, so the structure is not diagnostic for plant parasites.

The esophagus is the area between the stylet and the start of the intestine. The esophagus of plant parasitic nematodes will be variations of one of two major types. Shown here is a tylenchoid esophagus consisting of three areas: the anterior procorpus, midregion metacorpus or median bulb, and posterior basal glands or basal bulb. The median bulb facilitates transfer of digestive enzymes produced in the basal glands into plant cells and of plant products into the intestine. A two part esophagus is typical of dorylaimoid species and consists of an anterior cylindrical part and an expanded glandular posterior part.

Most of the body cavity or pseudocoelom is filled with intestine and with components of the reproductive system. The vulva is the opening of the female reproductive tract. The tube or tubes leading from the vulva have been divided by morphologists based on observed functionality into uterus, ovary, oviduct, seminal vesicle, etc.

There are both female and male nematodes, although not all species require the presence of males for reproduction, and in some species males are rare.

The tail of males may possess a number of structures such as spicules, gubernaculum, bursa or caudal alae which facilitate transfer of sperm into the vulva. The nervous system consists primarily of a nerve ring surrounding the esophagus with nerves extending from it to various locations.

A number of neurosecretory structures whose functions are not well understood can be seen on the cuticle (sometimes only by very good microscopists), including amphids, phasmids, and deirids.

Depending on the species, the excretory system consists of a simple excretory cell or a more extensive system of excretory canals. The excretory pore is the portion of the system most easily visible.

Nematodes do not possess respiratory organs or a circulatory system, relying instead on diffusion through the cuticle.

Variations in morphological characteristics have been extensively utilized to construct classification schemes for nematodes. These include variations in body shape, stylets, esophagi, location of the vulva and numbers of ovaries, head shape and lip configuration, amphids and phasmids, tail shapes, spicules, cuticlular ornamentation, etc.