Puppy question about crying

Question
Hello,  Thank you for taking the time to answer my questions.  I have an 8 week German Shep pup that I am crate training.  I had the pup for about 5 days now and he is "almost" house trained.  The crate is big enough for the dog to stand up, turn around, and lay down.  I have a Kong toy and I hide some treats in there too.  The dog was never create trained before, so it is new to him.  The problem is at night, he gets very upset and some what aggressive towards the cage.  I  do get up every 4 hours to take him out and when returning to the create I make it a positive experience.  The dog is experiencing separation anxiety at night.  I keep a light on, I put an old shirt in there so he smell my sent. I did not try to have some soft noise on yet.  What more can I do to help the transition
Thank you

Answer
You're doing the absolute right thing by taking this very young puppy out at night; most people don't bother to do this.  However, no 8 week old puppy can be reliably house trained; the ability to control urination does not physiologically exist yet.  This is a neonate (close to newborn) and he's at the beginning of a developmental fear phase.  Some of this behavior may be fear related (especially in the GSD); additionally, five days is nothing in terms of habituating a puppy to a new environment and building trust and a bond with the new owner.  To allay his stress (his aggression toward the crate concerns me, he's far too desperate and this is not a good age for this sort of behavior to develop), don't turn on any lights when you go to take him out of the confinement area during the night; keep it very low key, don't do anything to excite him or stimulate him, simply take him outdoors and praise his elimination and then calmly and quietly bring him back indoors.  Be careful about reward: if the puppy is stressed and anxious because you are leaving him and you pet him or offer a treat to attempt to create of your leave taking a good thing, you are inadvertently rewarding his fear.  You need to be able to read his body language.  Try this site and read her book, also:
http://www.canis.no/rugaas/index.php

Your puppy is not adjusting well to isolation and he's far too young to be so isolated.  The crate is also far too small.  You do NOT teach a dog to urinate outdoors by confining him to a space where he cannot eliminate without lying in it; a puppy this age is bound to have accidents and the more anxious he is, the more difficult it is for him to remain in this crate.  You need to bring this puppy into your bedroom or close by and put him in either a confined space (like the adjoining bathroom) or buy a much larger crate.  Put a soft bed and his kong toy in one corner; put newspapers under foot (NOT to paper train him but to absorb urine should he inadvertently produce it.)  The way to house train is to take the puppy out at fair and regular intervals (which you are doing) and REWARD/praise every outdoor elimination, while observing the puppy in the house (by confining him on very long, lightweight leash so he can't get out of your sight), interrupting any inadvertent lapse gently and then taking the puppy outdoors to finish.  If you persist in this method, your puppy will house train reliably (although many dogs can have accidents up to nine months of age), he will learn to be clean in his living space, he will learn you can be trusted and offer consistent leadership, and he will not develop separation issues that may lead to other unwanted behaviors (like confinement aggression.)

House training a puppy is the easiest part of puppy ownership.  The difficult part is SOCIALIZING the puppy to everyone, many variety of places, other animals, etc. on a daily basis throughout the first 18 months of age STARTING NOW or as soon as your veterinarian determines the vaccination history has provided protection.  POSITIVE REINFORCEMENT TRAINING must be used with any dog, but especially a breed like the GSD, and you can begin very, very short sessions right now.  Go to ClickerTraining.com for information.  A puppy kindergarten (conducted ONLY by an experienced positive reinforcement trainer) is a MUST.  Be sure to monitor the class first (your puppy is too young for this right now so it's a good time to start investigating) and be sure the puppies are all around the same age (for developmental behavioral reasons) and under control in terms of being closely observed.  Once your puppy has graduated to the next level you can participate in a beginner's obedience class using positive reinforcement ONLY.  Strong, kind, consistent leadership is absolutely required for this breed.