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Although it might seem a little morbid to leave the dead animals in with the mother and any surviving pups, removing the dead puppies might agitate the mother. She knows how many puppies she delivered and removing the dead ones may make her frantically start looking for her pups. Instead, leave the dead pups in with the mother for a while. Eventually, she will realize they are dead, allowing you to remove them without causing her distress.  Once the dead puppy’s body cools, the mother will likely notice that it is dead. If the mother is still trying to care for any dead pups after a few days, be sure to remove them even if it causes the mother distress. Parasites from the decaying carcasses can be passed on to the mother and the remaining pups. If the mother or surviving pups seem ill in any way, remove the dead puppies immediately. You do not want a parasite taking advantage of their weakened immune systems. After you allow the mother some time to notice that the puppies are dead, remove them from the rest of the litter. It may be best to remove the dead animals while the mother is not looking to prevent unnecessary agitation. You should use a paper towel or rubber glove to grab the carcasses so that you do not infect yourself with any parasites from the decomposing animals. Once you remove the dead animals, put them in a freezer bag and place them in the freezer. You should then contact your veterinarian about having the dead animals tested. It is important that you find out if the other litter members are at risk or if the mother has some health issue that may prevent her from breeding again. If you have the placenta, include that with the dead puppies.
Allow the mother to spend some time with the dead puppies. Remove the dead animals. Contact your veterinarian.