This is from "Bringing a Prarie Dog Pup into your home" by Karen Stocia, Betsy Callis and Lynda Watson
Scent Glands
All animals have some type or method of marking their territory.
Prairie Dogs have three secretory glands located in the opening of their anus.
The glands look like small pinkish tubes that protude when the prairie dog is excited, territorial or unsure of itself. The odor is similar to very dirty socks. It is not that strong and is only midly offensive. The secretions are waxy and minimal in amount.
Males that have not been neutered will have a stronger odor. Once altered, the smell will decrease and not be offensive.
Yound pups usually sent more often. This is related to the fact that pups are more excitable, inexperienced and have not yet matured. By the time they are 1 year old, you will have forgotten that your pet even possess this gland.
It is important to leave the gland intact. Some peole have tried to have this gland removed while the PD os being neutered or spayed. It is not necessary. The PD will only experience undue pain, possible loss of anal sphincter control, and potential complications such as not being able to eliminate stool.
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The book also shows your vet how to spay and neuter successfully. I really recommend buying this book. If you want a copy go look in the classifieds section under
exotic animals and you will see my ad for it. I have this book and read it all the time. Well worth the money.
Rhonda 
Only when they are REALLY scared do I smell anything, and that has only happened twice.
