In general, all reptiles are covered with scales. They can have four legs, or none. There are no snakes with legs, but there are lizards without legs. Thus, it is important to be able to distinguish a snake from a legless lizard. Snakes do not have eyelids. Lizards and turtles do have functional eyelids (with some exceptions such as some members of the gecko family). The snake eye is protected by a transparent scale called the spectacle. When a snake goes through ecdysis, or shedding, it will slough this spectacle with its skin. Occasionally this spectacle will not come off with the skin, and results in a retained eye cap.

A second obvious difference between snakes and legless lizards is that snakes do not have ears. But, to complicate matters, not all lizards have ears. Fortunately, all legless lizards do! The snake lacks not only the external ear, but also the middle ear cavity, tympanic membrane and eustachian tube. They do have an internal ear which functions in detecting motion, static position and sound waves which travel through the ground. Lizards and turtles lack external pinnae, but most have a conspicuous tympanic membrane. There are a few species of lizards which lack this feature.

Snakes and some lizards have a special sensory structure called the vomeronasal or Jacobson's organ. Its paired openings are just rostral to the choana. The flicking tongue picks up minute scent particles in the air and places them in direct contact with this organ.

There is a small opening caudal to the tongue called the glottis. Unlike mammals, the reptile glottis is always closed unless it is taking a breath. It forms a vertical slit in the closed position. Snakes are able to extend their glottis out the side of their mouth while they are eating to allow for respiration.

The trachea is usually long and is supported by cartilaginous rings. These rings are complete in the turtle and the crocodile, and incomplete in the lizard and snake. The trachea usually terminates just dorsal to the heart. In the lizard and turtles the trachea bifurcates into two bronchi which then enter the left or right lung. In the snake the trachea branches into a short left bronchus which terminates in a vestigial left lung. The size and functional capacity of this left lung varies from species, and can be complete in some of the water snakes where it is used for hydrostatic purposes. The right bronchus terminates in the functional right lung.

All reptiles, except the crocodile, lack a diaphragm. Breathing (inspiration and expiration) is accomplished principally by the intercostal muscles. These are assisted by other muscles of the trunk and abdomen, as well as smooth muscles in the walls of the lungs themselves.

The three chambered reptilian heart is composed of two atria and a large ventricle. There is an incomplete ventriclar septum which allows the heart to function as a four chambered heart.

Reptiles have a renal portal system. In the snake the parietal veins from the body wall and the caudal vein from the tail pass through the kidneys before anastomosing with the ventral abdominal vein. In the lizard the caudal tail vein and the internal and external iliac veins all feed through the kidneys before returning to the heart. In the turtle the renal portal system receives veins from the carapace, the musculature posterior to the kidneys and the external iliac veins.

Reptiles, except the snapping turtle, do not have lymph nodes. However, the lymphatic system in reptiles is complex. There is an extensive network of perivascular lymph channels around the major vessels and perivisceral lymph spaces which drain the viscera.

The spleen is a small, spherical, reddish organ located between the gall bladder and the pancreas. It is usually tightly adhered to the pancreas, and the two organs collectively are often referred to as the splenopancreas.

The pancreas is found caudal to the gall bladder on the mesenteric border of the duodenum. It has both endocrine and exocrine functions much the same as in mammals.