Training, training, training! I agree with Aart that the chickens are probably more afraid of the puppy because it's new. Chickens don't do change well, and they are a prey animal so their instinct is to be afraid of anything that they think might eat them. Keep puppy on a leash, correct undesirable behavior, and supervise any interaction for a very long time. Depending on the breed of dog, it could take months or more than a year for you to be able to trust your pup with the chickens. Our last dog was a black lab - great hunter, but never bothered the chickens. He was introduced to them at 8 weeks old, and as far as I know, never showed any aggression toward them. My current dog - a mutt that we believe is part Redbone Coonhound, Lab, and Golden Retriever - killed 11 of my meat birds when he was 6 months old. He just turned 2, and while he's good around them most of the time, I have had a chicken go missing here and there, and I'm beginning to think that he has picked them off. Not often, every few months or so. The reason I think this is because I saw him carrying a dead one into our woods one day when I drove in the driveway. He came out of the woods to greet me (without the chicken) and was acting all happy to see me. When I went out to the woods and found the chicken, he immediately put his tail between his legs and tried to crawl under my car. He knew he'd done wrong. After asking someone who's judgement I trust why he'd do that, I was told it could be from boredom or frustration. So, again - training, training, training, and close supervision for a very long time until you feel you can trust the dog.