The main artery of the mammalian circulatory system, the aorta is supplies oxygenated blood to the other arteries of the body. In humans, the aorta is about one inch in diameter and extends upward from the left ventricle, before arching downward through the chest. An opening in the muscular diaphragm termed the aortic hiatus allows the aorta to enter the abdomen, whence it divides into the paired common iliac arteries that extend into the legs. The wall of the aorta is composed of three tissue layers, the middle of which is thick and elastic. This elasticity enables the aorta to distend enough to accommodate the blood that surges through it as the heart contracts.

Much of what has been learned about the human brain has been discovered from research on the rat brain. Though smaller and less complex than that of humans, the rat brain is extremely useful as a subject of study because most regions of the brain are essentially the same among mammalian species. The rat brain has been heavily employed as an animal model for various neurological diseases, such as Parkinson's disease. In fact, it was studies of rats that led to the fundamental discovery that the Parkinson’s is caused by the loss of dopamine within the brain. Research with the rodents has also been critical in testing new drug treatments for the disease, as well as investigations of other potential therapeutic approaches, such as gene therapy.

Commonly referred to as the large intestine, the colon is a muscular tube-like component of the digestive system. The colon extends from the small intestine to the anal opening and is about five feet long in a human adult. Six main sections comprise the mammalian colon: the cecum, ascending colon, transverse colon, descending colon, sigmoid colon, and rectum. Though there are some differences in the function of the colon in different species, the organ primarily acts as a temporary repository for waste products and as a site of water absorption. A few vitamins are also absorbed by the colon, though no digestive enzymes are present in the large intestine and most nutritive components of digested material have been removed by the time this part of the digestive system is reached.

The diaphragm divides the chest cavity from the abdominal cavity in mammals through a partition of skeletal muscle and connective tissue. The breastbone and backbone serve as sites of diaphragm attachment as does a centralized aponeurotic tendon. Respiration is heavily dependent on the diaphragm, which is relaxed during exhalation and contracts during inhalation. When relaxed, the diaphragm is arched like a dome and is in close contact with the lungs and heart. In the contractile state, the partition moves downward, facilitating the expansion of the chest and reducing pressure inside of the cavity. In addition to its role in breathing, the diaphragm is involved in digestive processes and waste expulsion.

Three major regions comprise the small intestine: the duodenum, jejunum, and ileum. The region closest to the stomach is the duodenum, which is separated from that structure by the pyloric sphincter. Once matter is passed from the stomach to the duodenum, it is exposed to bile and digestive juices. These substances, which aid in food digestion, are released into duodenum via the hepatopancreatic duct. Movement of the bolus through the duodenum and other parts of the small intestine is driven by peristalsis, wavelike muscular contractions.

The reproductive systems of mammalian males contain a component called the epididymis. A narrow, coiled tube connecting each testicle to the corresponding vas deferens, the epididymis serves as a transportation tract and storage site for sperm. Male gametes are immature and incapable of egg fertilization when they leave the testes, but as sperm travel the length of the epididymis they mature, becoming capable of motility and achieving fertility. The maturation process is not completed, however, unless the reproductive cells enter the reproductive tract of a female.

A component of vertebrate digestive systems, the tubular esophagus moves food from the throat to the stomach. In mammalian species, the esophagus extends from the pharynx to the stomach. The role of this part of the alimentary canal is to serve as a conduit for food taken into the body. Wavelike contractions (known as peristalsis) of the esophageal wall force the food along length of the muscular tube. Mucus glands located in the wall help lubricate the food and ease its movement along the provided path.

Cardiac muscle comprises most of the mammalian heart, which also contains nerves, blood vessels, and valves. Cardiac muscle is striated in appearance, but unlike other striated muscle, controls an involuntary activity, the pumping of the heart. The rhythmic contraction of the heart muscle pushes blood through its chambers and into the connecting blood vessels. Oxygenated blood is transported away from the heart to other regions of the body via arteries, while veins are responsible for carrying oxygen-depleted blood to the organ. The sinoatrial node, commonly referred to as the pacemaker, controls the rhythm of the heart.

The last section of the small intestine is the ileum, which is divided from the large intestine by the ileocecal valve. The inner surface of the ileum is covered with small finger-like appendages known as villi. Epithelial cells that line the villi feature numerous microvilli, further increasing the surface area of the ileum. The large surface area of the structure is important for maximizing the adsorption of enzymes and the absorption of nutrients. Enzymes secreted by the epithelial cells are essential for the final steps of carbohydrate and protein digestion. Blood is supplied to the ileum by the superior mesenteric artery and its branches.

The central region of the small intestine, jejunum connects the duodenum to the ileum. The name of the structure derives from the Latin word jejunus, meaning “empty of food” or “hungry.” The term was chosen to reflect the fact that ancient physicians examining bodies after death found this section to be habitually devoid of food. In adult humans, the jejunum is approximately 8 feet long and about one inch in diameter. In order to fit in the abdominal cavity, it winds back and forth in a compact formation, as does the rest of the small intestine.

Most vertebrates, except for many fish and a few species of amphibian, utilize lungs for respiration. Air that enters the body through the mouth or nose eventually reaches the lungs after traveling through the trachea and the bronchi. The lungs are highly elastic organs composed of specialized cells that form millions of tiny air sacs termed alveoli. An extensive network of capillaries surrounds the alveoli, which are organized into lobules. Blood passing through the capillaries releases carbon dioxide into the alveoli to be exhaled from the body. Conversely, oxygen inhaled into the lungs diffuses from the alveoli into the bloodstream.

Rats are commonly used as animal models for the characterization of diseases that affect humans and for the evaluation of the effectiveness of potential treatment for those diseases. The rat mammary has been extensively employed in studies of breast cancer, one of the main causes of cancer-related death in women. Breast cancer is a form of cancer that arises in either the exocrine gland system or ducts that comprise the mammary glands. Incidence of breast cancer has been gradually on the rise since the 1970s, but at the same time detection and treatment has improved, resulting in a decline of mortality in recent years. Numerous risk factors for breast cancer have been identified, including a genetic factor associated with a mutated BRCA1 gene.

As producers and repositories of eggs, ovaries are central to the female vertebrate reproductive system. Homologous to the male testes, the ovaries secrete the female sex hormones estrogen and progesterone, as well as a number of other minor hormones. During embryonic development, the ovaries produce immature eggs, which mature and are released later in life after reproductive maturity has been reached. According to traditional scientific opinion, the eggs female mammals produce before they are born serve as their sole source of eggs throughout their reproductive years. However, recent scientific evidence obtained from studies of rodents suggests that this may not be the case. Whether or not humans can produce additional eggs postnatally is not yet known with certainty.

After leaving the ovaries, eggs travel through tubular oviducts to the uterus or to the outside of the body from the ovaries in egg-producing female animals. In humans, they are commonly referred to as fallopian tubes. The internal environment provided by the oviducts is conducive to fertilization of ova and the first stages of conceptus development. An egg enters an oviduct at the broad portion of the tube known as the infundibulum and moves along the tube with the help of the ciliated epithelium that lines it. The cilia beat with a wavelike motion, propelling a released ovum toward the uterus. When an egg is unfertilized, it typically degenerates in the ampulla, the mid-region of the fallopian tube. A fertilized egg will continue along the path, which terminates in the isthmus, the final portion of the oviduct before reaching the uterus.

A temporary structure found only in pregnant females of higher mammalian species, the placenta develops in the uterus and is attached to it until shortly after childbirth. The placenta is also connected to the fetus via the umbilical cord. Placental vasculature is extensive and enables the ready transfer of oxygen and nutrients to the fetus from the mother's circulatory system, as well as the disposal of fetal waste products. The placenta serves as a barrier to many harmful materials, providing a certain amount of protection to the fetus. Alcohol and most viruses are not successfully filtered out by the placenta and can be extremely detrimental to fetal development. The placenta also functions in a glandular and metabolic capacity. A number of different hormones are secreted by the organ, including progesterone, gonadotrophin, and estrogen.

In rats and other vertebrates, the large intestine contains three sections: the cecum, colon, and rectum. The terminal portion of the organ is the rectum, which extends from the sigmoid flexure (an S-shaped portion of the colon) to the anal canal. Compared to many other parts of the alimentary canal, the rectum, with a length of only about 5 inches in the adult human, is quite short. Thus it does not wind back in forth in the body as do the intestines, but stretches simply in a straight line toward the anal sphincter.

The seminal vesicles are paired sac-like glands in the male reproductive system. Positioned at the base of the bladder, the vesicles empty into the ejaculatory duct that leads into the urethra. The primary function of the seminal vesicles is to secrete much of the fluid that carries sperm. In humans, approximately 60 percent of seminal fluid is released by the vesicles, though this varies among mammalian species. The prostate gland is responsible for secreting most of the remainder of the fluid, which combines with mucus produced by the Cowper's glands to form semen.

Skeletal muscle exhibits an alternating light and dark striped appearance when viewed under a light microscope and is, consequently, often referred to as striated muscle. This type of muscle is typically under conscious control and comprises the majority of the body's muscle mass. Linked to the skeletal system, skeletal muscle also provides the basic shape of the body. The dark regions of skeletal muscle consist of Type I fibers, which employ oxidative metabolism and are especially adapted for activities that require endurance. The light regions are composed of Type II fibers that tire much faster but are useful for activities necessitating spurts of power or speed. Type II fibers utilize anaerobic metabolism rather than oxidative metabolism.

Due to the design of the rodent digestive system, most rodents must consume their food twice before nutrients can be efficiently absorbed. When food is initially imbibed by a rodent, it is softened in the stomach and is carried to the small intestine and then a large, post-digestive cecum that houses a dense collection of bacteria. The activity of the bacteria is breaks down cellulose molecules into simple starches and sugars, but once the material has reached the part of the digestive tract in which the bacterial flora is located, it is past the point where it can be absorbed into the body. In order to obtain nutrients that would be otherwise lost, the rodent reingests the fecal pellets it produces.

Functioning chiefly in metabolism and growth, the thyroid is a major endocrine gland present in craniate vertebrates. In humans, the two connected lobes of follicular tissue that comprise the gland are located on either side of the trachea, but the gland is positioned differently in various other species. The thyroid gland secretes thyroxine, a hormone that regulates the oxidation rate of cells and contains a large amount of iodine. Insufficient iodine in the diet can interfere with the production of thyroxine, resulting in hypothyroidism, which is distinguished by swelling of the thyroid and neck known as goiter. Hypothyroidism of this type has been virtually eliminated by the widespread use of iodized salt. The condition may also develop, however, due to problems with glandular function, in which case it is most commonly referred to as either cretinism (childhood form) or myxedema (adult form). Studies of the rat thyroid have been critical in developing a better understanding of these and other thyroid diseases.

Highly elastic and muscular, the tube-like vagina links the cervix to the vulva in the female reproductive system. In humans, the vagina is usually approximately four inches long and one inch in diameter. The size and shape of the vagina changes significantly during childbirth in order to accommodate the fetus as it is being delivered. At this time, the vagina is often called the birth canal. No glands are present in the vaginal wall, but secretions are produced by glands located near the opening of the organ.