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Always remember that you are dealing with a very immature young animal. Be realistic, flexible, patient and always fair during puppy training sessions. Your puppy doesn't just automatically know this stuff! It's all new to him and he is bound to have the odd slip up and mistake along the way. Don't worry about these mistakes, just move on and do your best to prevent them in the future.
Help him relax when he comes home. When your puppy gets home, give him a warm hot water bottle and put a ticking clock near his sleeping area. This imitates the heat and heartbeat of his litter mates and will soothe him in his new environment. This may be even more important for a new dog from a busy, loud shelter who's had a rough time early on. Whatever you can do to help him get comfortable in his new home will be good for both of you.
Unless you plan to keep your dog outdoors--and few of us do because it's not recommended--you'll need to teach your dog where to eliminate. Therefore, house training (also called housebreaking or potty training) is one of the first things you need to work on with your dog. Crate training can be a very helpful part of the training process. This includes house training as well as many other areas of training:

When your dog knows the release cue and how to sit on cue, put him in a sit, turn and face him, and give him a treat. Pause, and give him another treat for staying in a sit, then release him. Gradually increase the time you wait between treats (it can help to sing the ABC’s in your head and work your way up the alphabet).  If your dog gets up before the release cue, that’s ok! It just means he isn’t ready to sit for that long so you can make it easier by going back to a shorter time.
Teach him to come when called. Come Jasper! Good boy! Teaching him to come is the command to be mastered first and foremost. And since he'll be coming to you, your alpha status will be reinforced. Get on his level and tell him to come using his name. When he does, make a big deal using positive reinforcement. Then try it when he's busy with something interesting. You'll really see the benefits of perfecting this command early as he gets older.

Puppies develop very quickly during their first three months, particularly after their eyes and ears open and they are no longer completely dependent on their mother. Their coordination and strength improve, they spar with their littermates, and begin to explore the world outside the nest. They play wrestling, chase, dominance, and tug-of-war games.
Bring your puppy to the crate for naps and quiet-time breaks so that he can “unwind” from family chaos. Start in increments of 10 minutes and work up to longer periods. Offer treats when he goes inside, and distraction toys, like a stuffed KONG. For years, this author has been giving her Yorkie a treat every day as soon as he goes into his crate and sits. Now as an adult dog, he runs to his crate each morning in anticipation of the goodie.
Take it outside. Finally, you’re ready to test your puppy’s skills in the Great Outdoors. There will be new challenges with this step because all the sounds, smells, and sights your puppy encounters will be intriguing and new to him. Be patient and keep the first walks short. While you’re on a walk, if your puppy looks as if he’s about to lunge toward something or is about to get distracted (you’ll notice this because you will keep your eyes on him at all times), make your cue sound and move a few steps away. Then reward him with a treat for following you.
Just as a child needs a caring parent; an athletic team needs a coach; your puppy needs a leader and a clear social hierarchy. If you do not take up the role of leader, your dog will; and you will end up with an unruly, disobedient dog. Many people try to win their new puppy's love by letting the puppy always have its way. Buckets of affection is a wonderful thing for most puppies, but it must be tempered with respect.
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