The other answers may help if this dog is 'simply' misbehaving: ie, the dog is untrained and underexercised, and needs to be given exercise and taught when to go to sleep. The most important is safety. While it can affect all dogs, short-nose breeds like the Pekingese, Maltese, Shih-Tzu, pug and Chihuahua have a greater risk because of their shallow eye sockets. Puppies can easily get into trouble if your house isn’t puppy-proofed. Dogs with Lyme will often feel intermittent pain and scream when you touch them. This is behavior based and rooted in lack of training. Sometimes they’ll cry for a few hours before they stop. If your puppy is crying in her crate, get closer, but don’t take her out just yet. Your Chihuahua could be predisposed to it as they are part of the brachycephalic dog group. Chihuahua crying out in pain, but perfectly fine... Home » Training & Behavior » Chihuahua crying out in pain, but ... such as Lyme. Puppy Needs Food A crate protects household objects from sharp puppy teeth. They cry a little less the next night and the following night. I crate them at night to keep them safe and also to keep my sanity if they’re not housebroken, and they all cry at night. Chihuahuas are known to be stubborn, but they want to please their owners and earn rewards. When we’re talking about a whimper or whine, the canine “cry” can mean one of a million things. I’ve fostered many chihuahuas and some of them were puppies. Which is why interpreting a dog’s cry can be tough. There are good reasons to crate puppies overnight. Crating helps with house training too. Your Chihuahua might be suffering from Small Dog Syndrome. Young puppies may suffer from separation anxiety, have no idea when he needs a potty break and may end up crying all night. One way to know if the entropion your Chihuahua gets is inherited is if it occurs before the Chihuahua has turned one year old. If your Chihuahua has small dog syndrome, he will try to appear larger than life to let everyone around him know just how fierce he can be. Dogs are no different. Chihuahua puppies can be adopted out as soon as three months after they are born. This means that dogs with short heads and noses are more likely to get it. Yes, crying comes naturally to newborn pups just like newborn infants, but this can be a matter of concern if the crying is excessive and is practically unstoppable. Be visible to her until she falls asleep, then go back to bed. A dog that is deep in slumber enough to be crying or whimpering in her sleep is very deeply asleep. Spend some time near the crate if your presence quiets her. If your dog cries while sleeping, it is likely during the REM cycle, when your dog is most deeply asleep. The “cry it out” method can cause permanent neurological and emotional damage for your chihuahua puppy. According to TheNest, 20 to 25% of all small dogs develop tear stains. 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