Mouse Anatomy: Interactive 3D Model and Labeled Diagrams

The house mouse is a small rodent of the family Muridae, and the laboratory mouse is its domesticated form. An adult weighs roughly 20–40 g and is about 8–10 cm long from nose to tail base, with a tail of about the same length. Inside, it has the full mammalian set of organ systems arranged as in a rat and, broadly, as in a human: a diaphragm, a four-chambered heart, lobed lungs, a lobed liver, a pair of kidneys, and either testes and accessory glands or ovaries and a two-horned uterus.

Mouse anatomy has some features you will not find in a human. The incisors never stop growing. The stomach has a non-glandular forestomach. The caecum is large and there is no appendix. The left lung has a single lobe. The cerebral cortex is smooth, and the olfactory bulbs are huge. Females have five pairs of mammary glands and separate urethral and vaginal openings; males have a penile bone.

Directions: cranial (or rostral) is towards the nose, caudal towards the tail, dorsal the back, ventral the belly. Left and right are always the mouse's own.

Seen from the left side, the mouse's brain and olfactory bulbs fill the back of the skull; the heart sits between the lungs in a short thorax; behind the diaphragm come the liver (with the gallbladder), the stomach and spleen on the left, the kidneys against the back, and a belly packed with small intestine, the large caecum and the colon. In a female the ovaries lie behind the kidneys and the uterine horns run back to the bladder region.

The laboratory mouse is the most widely used mammal in biomedical research because it is small, breeds fast and, crucially, its genes can be changed and studied directly. The National Human Genome Research Institute summarises the genetic reason simply: mice and humans share virtually the same set of genes, and of thousands of genes compared only a handful are found in one species but not the other. A mutation that causes disease in people can often be recreated in a mouse. (National Human Genome Research Institute: why mouse matters.)

Anatomy is the other half of the story. A mouse has the same organ systems as a human, arranged in the same way, but some details differ: it has a forestomach, a large caecum, four main liver lobes, five lung lobes, a smooth brain with huge olfactory bulbs, a duplex uterus and a penile bone. Researchers have to know these differences to interpret experiments, which is why 'comparative anatomy of the mouse and human' is a subject of its own.

The mouse brain is the most mapped brain in science. Its main parts, front to back, are the olfactory bulbs, the cerebral cortex, the hippocampus, the thalamus and hypothalamus, the midbrain, the cerebellum and the brainstem. The diagram shows them in the two planes that atlases and lab papers use: sagittal (side) and coronal (cross-section).

A mouse brain weighs only about half a gram, but it contains the same major parts as a human brain. From front to back: two large olfactory bulbs, the cerebral hemispheres (whose outer layer is the neocortex), the hippocampus curled underneath the back of each hemisphere, the thalamus and hypothalamus in the middle (diencephalon), the midbrain with its colliculi on top, the cerebellum, and the pons and medulla of the brainstem continuing into the spinal cord. The surface of the cerebrum is smooth (lissencephalic), without the folds of the human cortex, so in a dorsal view the colliculi of the midbrain can often be seen between the cerebrum and cerebellum.

Brain atlases show the mouse brain in two standard planes. A sagittal section cuts from front to back, like the side view of the model, and shows the olfactory bulb, cortex, hippocampus, thalamus, midbrain, cerebellum and brainstem in a row. A coronal section cuts across the brain from side to side, like slicing a loaf, and shows left and right structures together; the hippocampus appears as a curled band under the cortex. The Allen Mouse Brain Atlas, the standard free reference, provides 132 annotated coronal sections at 100 µm intervals and 21 sagittal sections at 200 µm intervals. (Allen Mouse Brain Atlas: reference atlas (coronal and sagittal).)

The hippocampus is the structure most people look up. In the mouse it is a C-shaped structure that runs from near the midline at the top of the brain, back and down to the side (temporal) part of the hemisphere. It is essential for memory and for spatial navigation, and much of what is known about 'place cells' comes from rodents. The cerebellum sits behind the cerebrum over the brainstem; its central worm-like vermis and two hemispheres coordinate movement and balance.

The mouse heart has the same four chambers as a human heart: two thin-walled atria receive blood and two ventricles pump it, the right to the lungs through the pulmonary trunk and the thick-walled left to the body through the aorta. It lies in the middle of the thorax with its apex pointing back and to the left, covered at its base by the thymus. Like rats, mice keep both a right and a left cranial vena cava, while humans keep only the right (superior vena cava). The caudal vena cava returns blood from the hind body through the liver and diaphragm.

The main difference is scale and speed. A mouse heart weighs a fraction of a gram and beats several hundred times a minute, roughly ten times faster than a resting human heart. The mouse is still the main model for congenital heart disease, because the steps of heart development are shared.

The mouse liver is divided into four main lobes that can be further subdivided. Using veterinary names, a micro-CT study of living mice identified the left lateral lobe (the largest), the left and right medial lobes (together the 'median lobe' of many guides), the right lateral lobe and the caudate lobe with its caudate and papillary processes. Lobe size and the fusion of the medial lobes vary between strains and individuals. (Fiebig et al. (2012), Three-dimensional in vivo imaging of the murine liver: a micro-CT anatomical study, PLoS ONE (PMC).)

Unlike the rat, the mouse has a gallbladder. It is a small, thin-walled, greenish sac lying between the left and right medial lobes, which is why pathologists sample those two lobes together with the gallbladder in mice. It stores bile between meals. If you are comparing a mouse and a rat, the gallbladder is the quickest liver difference to find: organ-sampling guides for rodents list the gallbladder as present in mice only. (Ruehl-Fehlert et al. (2003), Revised guides for organ sampling and trimming in rats and mice, Part 1: liver and gall bladder (RENI).)

The mouse lung follows the rodent pattern: one undivided lobe on the left and four lobes on the right (cranial, middle, caudal and accessory). The accessory lobe tucks behind the heart. Humans have two lobes on the left and three on the right. The trachea, bronchi and diaphragm are arranged as in the rat. (Olivares Pérez-Montt & Gil (2016), Lobulación pulmonar de la rata blanca, Int. J. Morphol. 34(3).)

The mouse digestive tract runs oesophagus, stomach, duodenum, jejunum, ileum, caecum, colon, rectum. The stomach has a non-glandular forestomach lined with keratinised squamous epithelium and a glandular stomach, divided by the limiting ridge. The caecum is a large, curved, blind sac where bacteria ferment plant material; there is no appendix. The pancreas is diffuse and spread through the mesentery rather than a single compact organ. (NTP Atlas of the rodent stomach (forestomach, limiting ridge, glandular stomach), PDF.)

The mouse skull is long and narrow, with a large braincase, a pointed snout (rostrum), a zygomatic arch on each side and a rounded tympanic bulla over each middle ear. Like the rat, the mouse has 16 teeth: one ever-growing incisor and three molars in each half of each jaw (I 1/1, C 0/0, P 0/0, M 3/3). The incisors have enamel only on their front faces, which keeps them chisel-sharp as they wear, and the long toothless gap behind them is the diastema. (Hunt (1924), A Laboratory Manual of the Anatomy of the Rat, Internet Archive.)

The vertebral column has 7 cervical, 13 thoracic, 6 lumbar and 4 sacral vertebrae, followed by roughly 28 to 30 caudal vertebrae in the long tail. There are 13 pairs of ribs. Both girdles are complete, including a slender clavicle, and the tibia and fibula fuse in their lower half. The hind foot is long and the mouse walks on its soles (plantigrade). These are the same counts Hunt gave for the rat; caudal counts vary between individuals. (Hunt (1924), A Laboratory Manual of the Anatomy of the Rat, Internet Archive.)

The mouse eye is small, about 3 mm across, and bulges from the side of the head, giving a wide field of view for spotting predators. Its lens is very large compared with the eyeball and nearly spherical, leaving only a thin vitreous space in front of the retina. The retina is dominated by rods, as suits a nocturnal animal, and has no fovea. Albino strains have pink-red eyes because they lack pigment in the iris and retinal pigment epithelium. Behind each eye lies a large Harderian gland, which is often exposed when the eye is removed.

Research on mouse muscles concentrates on the hindlimb. A microCT and dissection study of female C57BL/6 mice identified 39 distinct muscles of the hindlimb and pelvis in nine functional groups. Among the best known: the quadriceps (rectus femoris and three vasti) on the front of the thigh straighten the knee; the medial and lateral gastrocnemius, soleus and plantaris on the back of the shank insert on the heel through the calcaneal tendon and extend the ankle; and tibialis anterior and extensor digitorum longus on the front of the shank flex the ankle and lift the foot. (Charles et al. (2016), Musculoskeletal geometry, muscle architecture and functional specialisations of the mouse hindlimb, PLoS ONE (PMC).)

The same study found that rectus femoris has the largest physiological cross-sectional area of any hindlimb muscle, with the lateral gastrocnemius second, and that muscles further down the limb have shorter fibres and longer tendons, suited to force and elastic energy storage. Gastrocnemius, soleus, tibialis anterior and extensor digitorum longus are the standard muscles sampled in mouse studies of muscle disease, exercise and ageing. (Charles et al. (2016), Musculoskeletal geometry, muscle architecture and functional specialisations of the mouse hindlimb, PLoS ONE (PMC).)

Female mice have five pairs of mammary glands: three in the cervicothoracic region and two in the inguinoabdominal region. Male mice usually have four pairs of rudimentary glands without nipples or collecting ducts. Rats, by comparison, have six pairs. In both species the anogenital distance is about twice as long in males as in females, which is how pups and adults are sexed. (NTP Nonneoplastic Lesion Atlas: mammary gland.)

Inside, a male mouse has paired testes in scrotal sacs (which can be withdrawn into the abdomen), the epididymis and vas deferens, large curved seminal vesicles with coagulating glands, a lobed prostate, bulbourethral glands, preputial glands and a penis containing an os penis. A female has small ovaries in fatty bursae, coiled oviducts, two long uterine horns joining just in front of the cervix, a vagina, and a separate urethral opening on a papilla in front of the vaginal opening. Pregnancy lasts about three weeks and embryos implant in a row along both horns. (Hunt (1924), A Laboratory Manual of the Anatomy of the Rat, Internet Archive.)

Between the shoulder blades of a mouse or rat lies a butterfly-shaped pad of brown adipose tissue (brown fat). Unlike white fat, which stores energy, brown fat burns it to make heat. Its cells contain many mitochondria with uncoupling protein 1 (UCP1), which lets the energy from food escape as heat instead of being stored as ATP: non-shivering thermogenesis. Because a mouse is so small and loses heat quickly, this interscapular depot matters a great deal, and it is studied intensively in obesity research. (Virtue & Vidal-Puig (2013), Assessment of brown adipose tissue function, Front. Physiol..)

Many students meet mouse anatomy through research procedures. The diagram shows the abdominal landmarks behind the standard intraperitoneal injection site described in institutional animal-care procedures.

An intraperitoneal injection delivers a substance into the peritoneal cavity, the space around the abdominal organs. It is a routine, regulated research procedure performed by trained staff under an approved animal-care protocol; this section explains the anatomy behind it, not how to do it. Institutional standard operating procedures place the injection in the animal's lower right quadrant of the abdomen, to avoid the urinary bladder, the caecum and other organs. The mouse is held with its head tilted slightly down so the abdominal organs slide forward, away from the site. (University of British Columbia Animal Care SOP TECH 10: IP injections in the mouse and rat, PDF.)

The right side is chosen because the caecum, the largest single loop of gut in a rodent, lies on the left. The bladder lies on the midline at the back of the abdomen, so the site is placed to the side of the midline. The same SOPs ask staff to draw back on the syringe before injecting: green material suggests the gut was entered, yellow fluid the bladder, and blood a vessel. (Virginia Tech SOP ARCD-0320: intraperitoneal injections in the rat, PDF.)

Mice and rats share a body plan; both differ from humans in the same ways. The table summarises the differences you are most likely to be asked about.

The rat is the usual animal for school dissections. For a step-by-step dissection guide with a worksheet and answer key, see our rat dissection page.

All 115 structures of the 3D mouse, grouped by system. This is the text version of the model: each entry gives what the structure is and what it does.