There are many reasons dogs can have mucous in their stools...colitis or IBD or even parasites like giardia. The first thing you should do is atleast run a fecal sample over to your vet for testing and proper treatment. Hope this sends you in the right direction and let me know if you have any other qustions regarding this :) If you have found this answer helpful, please remember to click the accept button. :)

Read more about giardia and coccidia here:

http://lbah.com/intpar.htm

Hi Gypsy,

The mucous normally helps lubricate the intestines. It indicates inflammation in the intestines when it is seen in the stool. Inflammation of the intestines can be cause by many things including parasites like worm (assuming your vet ruled this out with fecal test), protozoan infections like Gina mentioned which is giardia and coccidia (treated with different antibiotics), colitis, IBD which Gina also mentioned, a foreign object injested, unusual food or treat such as rawhide, bone, etc or even allergies.

The problem with giardia and coccidia is that they are hard to diagnose as while they do shed cysts into the feces which can be tested for, they only do this intermittently so at least 3 consecutive fecal samples are necessary to definitely rule them out. Treatment also does not necessarily wipe the infection out either. You can read about these in detail here:
http://www.peteducation.com/article.cfm?cls=2&cat=1622&articleid=727
http://www.missionmedvet.com/encyclopedia/giardia_canine.htm
http://www.beaglesunlimited.com/beaglehealth_giardiasis.htm

You can read about colitis and IBD on the following pages.
http://www.petplace.com/dogs/colitis-in-dogs/page1.aspx
http://www.petplace.com/dogs/inflammatory-bowel-disease-in-dogs/page1.aspx

And as I mentioned a foreign object, rawhide, unusual treat even grass can irritate the intestines and create excess mucous. Allergies can also seriously irritate the intestinal tract though usually there is other symptoms such as nausea or skin problems to indicate allergies.

And if your dog literally just got over giardia, then it is possible the intestinal tract is still a bit irritated and needs time to heal a bit. And if the yard or other area where there is standing water has not been eliminated, your dog can become reinfected again.

I hope this information helps explain how it is still possible for your dog to have mucous in the stool. You may want to start your dog on a bland diet for a few days of boiled chicken and rice to give his intestines a break before starting gradually back on dog food. I hope this helps.