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. The teeth of snakes and lizards are both acrodont (attached to the bone) and polyphyodont (capable of having several sets throughout life). Turtles do not have teeth, but instead, they have a horny beak which they use for biting. Non-venomous snakes have four rows of upper teeth: two rows on the maxilla and two rows on the palatine-pterygoid bones. There are only two rows on the lower jaw, one attached to each mandible. Venomous snakes substitute fangs for the maxillary teeth.

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 ventricular 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.

The single or double lobed thymus is found craniolateral to the thyroid gland, closely associated with the vagus. It does not involute when the animal matures as it does in higher vertebrates. Just caudoventral to the thymus is the thyroid. It is a spherical reddish-pink structure cranioventral to the heart and ventral to the trachea.

Reptiles have one or two pairs of parathyroid glands which can be found either cranial or caudal to the thyroid. In turtles the glands may be found imbedded in the thymus. These glands are difficult to find and are often obscured in the adipose tissue.

All reptiles have a pair of adrenal glands. They are found closely associated with the gonads and urogenital structures of the lizard and snake and with the kidneys in the turtle. The adrenals are pinkish filiform structures found medial to the gonads. Unlike mammals, the medullary and cortical tissue is indistinguishable, but nonetheless still produces the appropriate hormones.

For the most part the mouth does little more than catch the food. Very little mastication, if any, occurs. The saliva that is produced has little digestive significance, its role being mostly lubricatory. The esophagus has a special adaptation of several longitudinal folds which allow for great distensibility of the gut to accommodate large food items. The esophagus is dorsal to the trachea and extends from the pharynx to the stomach.

The stomach of the snake is fusiform, and in the lizard and turtle its shape grossly resembles the mammalian stomach. The stomach is rather short in the snake. Its junction with the esophagus is clearly noted at a site approximately equal to three-fourths the length of the liver. The stomach ends in a stricture, the pylorus, at the pyloroduodenal junction.

The small intestine may be either straight or have short transverse loops. The small intestine in the lizard and turtle has many loops and convolutions much the same as in the mammal. The small intestine terminates at the ileocolic junction. A cecum is present in some snake species. A cecum is present in both the lizard and the turtle.

The large intestine terminates at the cloaca. It is a short, straight tube. As in the bird, the reptilian cloaca has three chambers. The feces are discharged into the anterior chamber called the coprodeum. The next, or middle chamber, called the urodeum, receives the urogenital ducts. The posterior proctodeum acts as a general collecting area for digestive and excretory wastes. The male intromittent organs open into this compartment, and both the male and the female have scent glands which also open here.

The reptile has a metanephric kidney. It is situated in the posterior part of the body positioned adjacent to the body wall, with the right kidney anterior to the left. They are brown in color and consist of twenty-five to thirty lobes.

Since the snake lacks a bladder the ureters enter directly into the urodeum. The lizard and turtle the ureters enter the bladder, which then empties directly into the urodeum.

Both the male and female gonads are found in the posterior half of the body. They are medial to the kidneys and in the snake, the right is cranial to the left. The testes are off-white to yellow, and the ovaries are a yellowish pink.