One of the most popular methods of housebreaking dogs today is the use of crate training. Like most animals, dogs instinctively try to avoid soiling their own dens. The crate training method makes use of this instinct by confining the dog in an artificial "den" when it cannot be closely supervised. Because the den instinct is common to all canines, this method of housebreaking is highly effective for all dog breeds and even for Wolf-dog hybrids.

The "crate" is most often a plastic dog carrier, although other kinds of small, comfortable enclosures can be used. It must be large enough for the puppy to stand and turn around comfortably, but not much bigger; if the crate is too large, the puppy will simply eliminate in one end and sleep in the other end, defeating the purpose. As long as the crate is comfortable and the puppy is introduced to it gradually and is taken out to receive plenty of attention every day, most puppies will not only grow accustomed to the crate but actually become fond of it. Many dogs voluntarily continue sleeping in their crates long after they have been fully house-trained and no longer require confinement.

The puppy must not be confined in the crate for long periods of time. Most puppies under the age of about six months are incapable of waiting long periods of time for a chance to eliminate. If the puppy repeatedly finds itself forced to eliminate in the crate, it will eventually lose the inhibition against soiling its den entirely - making house-training much more difficult. The puppy must be taken outside to eliminate at least once every two to four hours during the day. In addition, it will almost always need to eliminate shortly after eating a meal or drinking water, after waking from sleep, after being removed from its crate, and after play or exercise. The owners also closely observe the puppy's body language and take it outside every time it shows signs of being ready to eliminate, such as squatting, walking in small tight circles, or sniffing the ground as though searching for the ideal spot. They only use this body language for a few seconds before they eliminate, so careful watch on the owner's part is needed.

If the puppy is caught in the process of urinating or defecating indoors, the owner should make a sharp, loud noise. The purpose of this is not to punish or frighten the puppy, but to startle it so that it will stop. The owner should then take the puppy outside through the same door or to some other designated area to finish the process. It is very important that after the dog has relieved itself in the appropriate area, it should be warmly praised and offered a treat, to make going outside seem like a very good act to do. If the puppy does not eliminate itself after 15–20 minutes of being outside, the owner should return it to its crate and try again later.

In the wild, all the dogs or wolves in a pack urinate and defecate in a designated area, away from the den. With housebreaking, the puppy comes to understand that the designated area for elimination is outside. The puppy will begin going to the door when it feels the urge to eliminate. The owner watches for this behavior and, when he sees it, praises the puppy and immediately lets it outside. If the door is not opened quickly, most puppies will spontaneously whine, bark or scratch at it to get their owner's attention; some owners may even train the dog to ring a bell when it needs to relieve itself. As the puppy grows older, it gains the ability to control its bowels and bladder for longer periods of time, and becomes increasingly able to wait long periods without requiring confinement. The amount of hours a puppy can hold its bowels is approximately equal to the number of months of its age. For example, if a puppy is 5 months old, then it can usually hold for 5 hours. This is true until the puppy is 10 months old, when 10 hours is the maximum time for any age. However, some breeds, especially the basset hound and many of the toy breeds are harder to housebreak than others. If a puppy seems not to be able to hold it very long (e.g. only 1 hour when they are a year old), then the puppy should be examined for bladder problems by a vet. One decided advantage to housebreaking a dog is the choosing of the proper breed of dog. Some breeds such as the hound family can be rather difficult to house break due to the natural instinct to be overly excitable.

You may also look up about other ways to potty train your puppy.

Most experts advise against punishing dogs when they defecate indoors, at least during the early part of the housebreaking process. This is not because they believe all punishment is necessarily inhumane, but because it can very easily create more problems than it solves. If a dog is punished for urinating or defecating, especially before it really understands where it is supposed to defecate, quite often it will simply learn not to defecate when people are watching. It may actually begin to avoid defecating when its owner brings it outside. Then, when the dog is indoors, it will look for an opportunity to hide and relieve itself, creating a mess in a place where the owner may not find it for some time. This can make house-training much more difficult than it needs to be.

Another extremely common mistake is for owners to punish a dog for eliminating in the house when they have not actually caught the dog in the act. If the owner finds a mess on the floor and goes to find the dog and scold it, the dog will believe it is being punished for whatever it was doing when the owner found it. Dogs are totally incapable of associating the punishment with their earlier actions, even if their owner drags them to the mess and points it out to them. Punishing a dog when it cannot understand what the punishment is for only makes it confused and upset, possibly creating entirely new behavioral problems.

One traditional method of punishment - rubbing the dog's nose in its own mess - is particularly counter-productive. As noted above, dogs and wolves have a natural urge to defecate where the rest of their pack does. They locate the spot by scent; this is why dogs will generally spend some time sniffing the ground before they relieve themselves. Thus, rubbing the dog's nose in its urine or feces actually reinforces to the dog that it should continue eliminating in that particular spot.