I have a 10 week old pup that has bloody (bright red) diarrhea. I have taken her to the vet, along with a stool sample. The good news is that nothing was found in the stool, no bacteria, no worms, nothing. The vet prescribed Flagyl 4 days ago. The bad news that it doesn't seem to be working. I have phoned my vet about my concerns, only to be told give the pills time to work.
She is eating, drinking and is normal happy pup. There must be something more I can do for this sweet girl. Any suggestions?

Fecal can come back negative and there still could be bacteria. Have your vet give you Alban and give that a try.

Flagyl is a high powered antibiotic which works fantastically in the GI tract...however, parasites are not bacteria.

I agree, try Albon....recheck the stool.

we had a litter and mom that suddenly started having bloody diarrhea, mom much worse than the puppies. I came home from work to the worse mess I have ever had to clean up. Took mom to the vet with stool and the vet said that most likely hook worms. We have never had an issue with hooks before but wormed everyone and within a two days all fine. Vet said not always seen in the stool. I doubt that anything would show up in the stools now since they have been on the antibiotic already. I would worm everyone for hooks if the stools are like reddish/brown runny pudding with no formed stool at all, smelly too like blood smells. If there is some form but just loose or watery with blood streaks then maybe the Albon would be a good choice. May be Coccidia, they don't always see that in stool either.

Thank you all for your help.
I tried Albon first, didn't do any good, bit like the Flagyl. I agree, sounds like another stool sample testing is in order, despite the fact that I was told that it isn't Coccidia, or any other of the ususal problems. I was told her problem lies within the colon.

My experience with coccidia and giardia it is often like looking for a needle in a haystack if you are relying on the tests. I don't understand why some vets won't treat without a positive test. You should still test but if the tests are inconclusive, play the odds. The treatments are effective and do not have significant side effects.

Albon or Marquis for coccidia
Panacur for giardia (but for 7 days and not 3)

Bright red blood indicates a bleed lower in the G.I. tract, like large bowel.
Bloody diarrhea should always be taken very seriously. Repeatedly self-treating for different parasites is not recommended because if it's something other than parasites, like a perforation or colitis, you are delaying appropriate treatment.
Puppies are notorious for eating inappropriate things that can cause damage to the intestines.
If the Flagyl has not been effective, I'm in agreement with you that the vet needs to work this up more to determine what is bleeding and where.
Good luck with your baby girl!

I have a boy with inflammatory bowel disease.

I would take your pup to an internal medicine specialist for an evaluation and consultation.
The longer symptoms continue, the more difficult it is on the pup, it's more difficult to treat, and difficult on you and your pocketbook.
If what you have done already has not worked I would not be messing around...
Praying your baby heals soon.

While they are checking for those other more serious things, or after they have checked and found nothing, is it harmful to use Marquis, Albon or Panacur? Nobody should ignore blood and self treat. My point is that a few vets trust parasite stool tests which are notoriously inconclusive and do not use common sense.

Over the years, there were 2 pups who I am specifically thinking of who each had hundreds of dollars of procedures. Neither had been treated for parasites (after leaving our home) because the tests were negative. Testing for parasites was the first thing the vets did. Finally, we convinced one of the owners to get some panacur because we knew we had just previously had some trouble with Giardia and suspected the pup may have left here with it. We had been saying this all along. The pup cleared right up. The other had coccidia really bad (again probably caught it at our house even though we had treated). We gave the owner some albon and cleared it right up.

But again, both vets refused to treat because tests were negative. Positive parasite tests can be trusted. Negative tests can not be.

Agreed that sometimes parasite checks need to be repeated to catch the parasite in it's diagnostic life cycle stage. This doesn't mean the tests don't work.
My point was: don't treat with drugs that may cause further problems, without a diagnosis. Is it harmful to use Marquis and Albon? Potentially, yes. Panacur is pretty benign and probably wouldn't cause additional problems, but it is not right to guess what parasite this puppy has without repeated testing.
Hopefully this puppy is better, if not, more diagnostics would be needed.
OP, keep us posted on your little one.

The pup has been on flagyl for 10 days with some improvement. A 2nd stool sample was taken to the vet. After 4 days they came back with Klebsiella and said it was most likely from eating wood shavings in the bedding. We don't usually use shavings but our supplier was out of the horse pellets and we had to have something. Has anyone had this kind of problem?

I have used wood chips (Cedar) for the last 7 years and I haven't have that problem. It is possible that the source of yours was contaminated.

Klebsiella is a type of bacteria, and is fairly common. Whether it was actually in the shavings or the puppy was ingesting shavings that had remnants of poop on them and she got infected that way, hard to say.
Did your vet say that Flagyl would take care of the klebsiella overgrowth? It may respond better to an antibiotic that is specific for klebsiella as Flagyl is actually an anti-protozoal, not an antibiotic.

Baytril is another antibiotic used for klebsiella. Always speak to your vet if you're looking to change antibiotics in case flagyl isn't working.

Baytril is not safe for puppies.