Puppies have an instinct to never be alone. In the wild, a lone puppy usually winds up being a dead puppy very quickly, so they cry in order to attract the attention of the pack. This is a very strong instinct to try and suppress for puppies living in homes. But there are ways to make the puppy feel not so alone and therefore more likely to be quiet.
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New Puppy
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If a puppy has just been taken from the litter and brought to a home, that puppy is going to begin to cry for the company it was always used to having. Placing a ticking clock under a blanket in the puppy's bed can help simulate the sound of the mother's heartbeat. There are products available that look like stuffed animals with ticking heart noises inside of them made specifically for very young puppies. If the puppy is not allowed in the bed, then placing the puppy's bed or crate in a bedroom within sight of a person can help to calm the puppy.
Daytime
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If the puppy is left alone for long periods in the daytime, try turning on the radio or television in order so the puppy hears voices. Leave an old, unwashed piece of clothing that you have recently worn in the puppy's bed or crate. The smell of you will comfort the puppy. It is also good to leave chew toys in with the puppy so that the puppy will have something else to do with his mouth other than cry. Keep a special toy just for when the puppy is to be alone so that they can associate being left alone with a good thing.
Reinforcement
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According to "Good Dog U" (Animal Planet, 1999), puppies who have a problem crying when no one is home need special training. This is called separation anxiety. Pretend to go to work. Go through all of the routine and then come back to the home in a couple of minutes. Open the door and if the puppy is crying, clap your hands and say, "No" in a low voice. Step out and shut the door. If the puppy is still quiet one minute later, open the door and give a food reward. Also, instead of letting the puppy follow you all around, train the puppy to stay on a bed so the puppy gets used to being alone.
Exercise
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According to "The KISS Guide to Raising a Puppy" (Liz Palika, 2002) puppies need a half-hour brisk walk every day and several play sessions with toys or romping about a yard in order to get tired enough to sleep at times when they have to be alone.
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