The Rat Fan Club

How to Do a Rat Autopsy

by Debbie “The Rat Lady” Ducommun

updated 5/18/11

Warning: This page contains graphic pictures of rat autopsies.

Note: The word “autopsy” literally means “self seeing” and technically is only applied to human bodies. Veterinarians use the term “necropsy” which means “dead body seeing.”  However, personally I prefer to use the term autopsy as more people are familiar with it, it doesn’t sound as gross as necropsy, and I like to think that rats are much like little people.


Much is known about disease in lab rats, but not as much is known about disease in companion rats.  Unfortunately, few rat owners choose to have autopsies done on their rats.  Even when the cause of death seems obvious, say respiratory disease, the real cause may be different.  For example, I’ve found that heart disease often mimics respiratory disease in rats.  I try to do at least a gross autopsy (which is just looking at the organs and takes only a few minutes) on all rats that I can.  I’d be happy to do a gross autopsy on your rat if you’d like to send me the remains.  I can then bury them here, or return the body to you.


I know that some of you don’t like the idea of having an autopsy done on your rat, but please do consider it.  Once your rat has passed on, the remains are not your rat any longer, only the vehicle that your rat occupied.  If your rat dies of an unknown cause, I urge you to have an autopsy done and let me know the results so we can gather more information on disease in rats.  It’s possible that an autopsy can later help another rat who is having the same symptoms.


Some vets may be willing to do a gross autopsy for free.  However, in some cases to really know the true cause of death, organ tissue samples must be sent to a pathology lab which can be fairly expensive.  Some labs offer a special low price for low-income people, so ask your vet about this possibility.  If you plan to have an autopsy done, and cannot get your rat’s body to the vet right away, do not put it in the freezer, which will damage the cells.  Instead, after sealing it in a zip-lock bag, place it in the refrigerator.  Then get it to your vet as soon as possible.


Doing a rat autopsy is very easy.  Of course, I understand that most of you are not going to want to do an autopsy, especially on your own rat, but I want to make the information available.  Perhaps the information will be useful to your vet, or perhaps you have a friend with a scientific bent who would be willing to do it for you. 


A gross autopsy consists of examining all the organs to see if their size, color, shape, and texture is different from normal.  In most cases, this will reveal the major cause of death.  In some cases, tissue pathology will be necessary to identify the major cause of death, or contributing causes.  For this, small samples of all the organs are needed.  It is best if the samples are placed in a formalin solution (ask your vet), but if necessary they can be placed in rubbing alcohol.  The samples should be taken gently to avoid damaging them.



There are only a few tools you need to do a rat autopsy.  You need a pair of sturdy scissors with a sharp point, a pair of tweezers or forceps, a pair of needle-nose pliers, and gloves.  For measuring, you’ll need a ruler marked in mm.  For measuring the heart inside the chest, it helps to use a tool called a drafting divider (see the tool at the bottom in the picture below).  You place the two sharp ends of the divider on either side of the heart and the divider holds that distance so you can then place the divider on the ruler to measure the distance.


It’s a good idea to take notes during the autopsy, otherwise it can be difficult to remember everything.  Here are some terms which are useful in describing an autopsy:  lesiona tissue change; massa tumor

texturesbrittle, caseous (cheese-like), firm, friable (easily broken up), gelatinous, gritty, hard, rubbery, soft, watery

severityminimal, mild, moderate, marked.




Starting the Autopsy

First examine the whole body and feel for abnormal lumps or lesions.  Next I recommend checking to see if there was a pituitary tumor. There may be a tumor present even if it was not yet causing symptoms.



   Step 1                                               Step 2                                        Step 3                                                Step 3


Lay the remains on the belly.  Step 1: With the scissors, cut the skin on the top of the head from between the eyes to between the ears.  Spread the skin apart until you can see the top of the skull.  Step 2: Place the pliers on either side of the eye sockets and crush the bones between the eyes.  Step 3: With the tweezers or forceps, start to remove the pieces of bone from the eyes to the back of the skull.  Gently insert the tool under the bones to lift and break them up.  Step 4: Once you reach the large bones forming the top of the braincase, work on one side at a time.  Apply pressure to get them to separate in the middle and break on the sides so they lift up like the top of a cardboard box.  This will expose the brain.  Step 5: Gently slide the tweezers or forceps under the front of the brain, lift it up, and remove it.  It helps if you turn the body on its side to take advantage of gravity.  If a pituitary tumor is present, it will appear as a dark red blob in the center of the brain cavity.  If there is no tumor, the bottom of the cavity will feature two ridges.  I then replace the brain, fold the bones back in place, and pull the skin back to cover them.



  Step 4                                                Step 4                                          Step 5



This picture shows the inside of the skull with the brain removed.           This photo shows the brain pulled back revealing a very large and

The small pituitary gland can be seen between the 2 ridges.                    obvious pituitary tumor.


Step 6: Turn the body over on its back.  To open the abdomen, start cutting at the lower portion.  You need to cut through both the skin and muscle.  Make the incision as long as possible. 

   Step 6


Step 7: Examine all the organs.  To check the texture of a tissue, cut it open. When you have more experience it will be easy to see abnormalities in the organs.  Check for tumors and note the location, appearance and size.  Fluid in the abdominal cavity is usually due to cancer or long-standing liver disease.




This picture shows the view when you first open the abdomen.  The large dark red organ at the top is the liver. Just below it on the right is the stomach, with just the tip of the dark red spleen visible at the far right, and on the left are the small intestines. The large greenish structure is the cecum, part of the large intestines. In rats who haven’t been eating much, the cecum is usually abnormally small.


This picture shows most of the deeper abdominal organs after the intestines have been pulled up out of the way.  The other kidney and ovary are on the

other side out of sight.  The spleen has been pulled over to the left of the picture but is usually between the stomach and kidney.  The other organs not visible are the bladder (at the base of the uterus), the pancreas (between the stomach and spleen), and the cecum (lower right abdomen).



This picture shows a good view of the entire uterus         

(which is shaped like a Y) and ovaries with the other    

abdominal organs pulled back out of the way.               


This picture, which was taken at an angle, shows the auxillary male reproduction organs.

There are 2 seminal vesicles and one prostate, which is attached to the bladder.



Step 8:  To open the chest, continue to cut as far forward as you can, slightly to the side of center to avoid the sternum.  Cut through the ribs and spread them open. Observe the lungs. Observe the heart in place, and measure its length and width.  This is easiest to do with the help of a measuring tool called a drafting divider as it is hard to get a ruler in the chest (see tools above).  You want to measure the heart in place in the chest because if the heart is abnormally enlarged, it will usually shrink once it is cut free of the aorta.


In this picture, the front of the chest with the ribs has been removed for a better view. This heart is fairly normal looking, although somewhat larger than normal.   The liver does not look healthy, and was probably the cause of death for this rat. (The purplish area on the right side of the lung is just a shadow; the picture has been flipped 90 degrees.)



This heart has an enlarged right ventricle.           This heart has a huge enlarged right atrium

Can you see how it has ballooned out? It             which is caused by high blood pressure

is so expanded it extends across the top              in the lungs.

of the heart.                                                                 



Step 9: Cut the heart out of the chest and cut it in half longitudinally to measure the width of the left ventricle and the thickness of its walls.


This is a normal heart showing the normal size       This heart has a mild case of hypertrophic                   This picture shows a heart with a

relationship between the left ventricle and the        cardiomyopathy, where the walls of the left                 greatly enlarged right ventricle, which is

thickness of its walls.                                            ventricle become thickened, narrowing the left            caused by high blood pressure in the                  

   ventricle.  This picture also shows the right ventricle    lungs, as well as some thickening of the

   which pumps blood to the lungs.                                 walls of the left ventricle. (The black stuff

                                                                                    is blood clots.)


Step 10: Once the heart is removed you can more closely observe the lungs and note any abnormalities. 



This picture shows lungs with severe                  This picture shows lungs that are completely

emphysema, and in front, the typical                   filled with small abscesses.  This is common

cobblestoning” caused by mycoplasma.             in rats with untreated respiratory disease.

                                                                        Can you believe this rat lived up until now?


For more autopsy pictures of lungs, click here.


When the autopsy is finished, the incisions can be sutured closed if desired.


Here is a chart detailing the most common abnormalities seen:


Organ                          Usual Abnormalities                            Possible Disease


Large intestines                         redness                                     inflammation. 

(Depending on length of time since death, may be bloated due to decomposition.)


Small intestines                          redness                                     inflammation


Uterus (unspayed female)          redness, swelling, pus                 infection, typically mycoplasma


Seminal vesicles                        yellow rubbery matter                prostate disease?

(unneutered male-neutering causes them to shrink to 1/3)


Prostate (male)                        enlarged                                    prostate disease


Bladder                                    overly full                                  urinary blockage


Kidneys                                    speckled, grayish pink, rough      degeneration


Spleen                                     enlarged                                    non-specific sign


Liver                                        enlarged, spots, swollen              infection, degeneration

(Speckling may occur due to decomposition)


Stomach                                   empty                                       poor appetite

                                                bloated with air                          respiratory distress


Heart, exterior                           enlarged                                    dilated cardiomyopathy


Heart, interior                            thick walls                                 hypertrophic cardiomyopathy


Lungs                                       expanded and enlarged              emphysema

                                                raspberry” texture                    mycoplasma

                                                large abscesses                         mycoplasma

                                                spots of pus, mottling                 pneumonia

                                                dark red                                    pneumonia, shock

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