Kathy has just gor two new puppies and is experiencing difficulties:

“We just got two 7 week old puppies - on is a Shih-Tzu and the other a Yorkie. I am having a hard time crate training them. We are putting them each in a “kennel taxi” at night with a towel, a toy and a wind up clock. The Yorkie doesnt make much noise but the Shih-Tzu will whimper off and on during the night. I check each of them atleast twice each night and they both poop in their crates. I know they are puppies, but what can i do to help them understand they cant sleep in their poop? We will be having to leave them alone during the day and dont want them to be sitting in their poop all day. We also put their crates out in the day time for them to get use to them, but they would just go inside and poop. Are we using the right kind of crate? HELP!!!!”

I don’t really want to make assumptions, but did you by any chance purchase your pups from a pet store or perhaps a newspaper ad? If so, this could be the cause of your problem.  Many pet stores get their puppies from “puppy mills” (also known as “puppy farms” outside of the US).  These places do not provide the best start for any dog, and they often have health and behavioral issues too.  To get an idea of the conditions a lot of pet store puppies will have been born into, take a look at this site: Puppy Love (it is a UK site, but the practice is the same throughout the Western world)  You can also see a flash slideshow with audio narration from the Humane Society of the United States here: HSUS: Inside a Puppy Mill.

What I would suggest is that you try and paper or pad train the pups (my free housetraining guide will help with this).  Instead of a crate, confine the pups to a larger area by either getting a puppy pen or leaving them in a small room like a bathroom or kitchen area.  Because they have already started bad habits, you may be as well using special toilet training pads that contain a scent that encourages the dogs to use that area to toilet.  Put the pads as far away from their beds and food bowls as possible. This will teach them that bed and toilet areas are different .  Once you have got them to go regularly on the pads, you can go back to crating them (make sure the crates have been cleaned of all traces of pee and poop using a sanitizer that eradicates pet odors) and progress to outdoor training if that is what you originally intended.