I am just about at my wits' end here and I have gotten some encouragement on this site, but still feel that I am not sure I'm doing everything I can to help my ~14-week-old pup Samson (we aren't quite sure how old he is because he is a rescue puppy).

He is a Rottie/Shepherd mix that we rescued/adopted from the SPCA. He has a great personality and we enjoy him (most of the time). Some background info that may be relevant - four days after coming home with us, I got a call from the SPCA that his sister had parvo. He ended up getting sick as well and came close to not making it. He did make it, though (yay!) and is now healthy and happy.

Our housebreaking/crate training efforts were definitely interrupted by the illness, but he is happy and quiet most of the time in his crate and we ignore whining and barking behaviors. The problem we are having (and had before he became ill) is pooping and peeing in the crate. The home he came out of before the SPCA was not a great environment and I'm sure is contributing to some of the problem we're having now. Most of the time, he is not left for hours on end as I have a flexible work schedule and can come let him out. When we leave him - it can be for 45 minutes or 5 hours - he frequently pees and poops in the crate. This in and of itself would be frustrating, but he also appears to lay in, roll around in, step in and generally cover the entire crate area with feces. As I said, he can accomplish this in as little as 45 minutes. He enjoys his crate and will usually enter it willingly with little objection (he gets a treat) and he'll sometimes whine for a minute or two after the treat is eaten, but then calms down and rests or plays quietly.

We now have him on a fairly regimented eating/watering schedule and take him for 1-2 walks before putting him in his crate when we leave for work and we're switching him to all-natural kibble (Chicken Soup...). The problem has, however, persisted and we have at least one of these incidents per day. When he is out of his crate playing with us (we do not allow him to be out of his crate unless he is interacting with us), he will usually go to the door to let us know he needs to go out and then will do his business outside, but if he is left in his crate and we are not here to get him out, he will poop. He has made it as long as 6 hours during the day without pooping, but as I mentioned, he has messed the entire crate in less than one hour. As an aside, he only pees in the crate occasionally - pooping appears to be more frequent.

Any thoughts/advice or encouragement? Thanks in advance to anyone who reads all of this and responds. It is greatly appreciated!

You said the pup is 14 weeks old.........how big is the crate you are using? If the crate is too big, then sometimes a pup will poop or pee in one end of it.

You only need to have enough space for them to turn around and sleep in it, so with that said if you are using a crate that's too big then you should use a card board box or seomthing to take up the extra space.

I use two different size crates for raising a pup. I start off with the smaller one, and then as he grows, I switch to the bigger one.

it could be an anxiety behavior if he isnt hardly peeing in the crate, however he is pooping in the crate, try to let him out of the crate as often as you can and go straight outside, and give him plenty of time to go do his thing, i was also going to ask if he was eating his feces when he is pooping in the crate and smearing it all over, some say that they are trying to 'clean' up after themselves, just a thought, be patient with him, and dont punish him for relieving himself anywhere, just dont give him very many chances to make mistakes, and he will eventually go outside because he prefers it there...JMO

The crate is the right size, although I did try making it smaller when he initially came home - it didn't make a difference.

He's gone for as long as 6-1/2 hours during the day with no problem, but other times he doesn't make it long at all. This is gross, but I usually try to see if the poop is still warm when I get home and it's usually not.

I think part of the problem is that he poops like 5-7 times a day. We're hoping a more nutritious (all natural) diet will help with this. If we are gone at all during the day, we are likely to miss one of those 5-7 times.

We're still feeding 3 times a day - any thoughts on whether 2x might help?

I might be all wet here, but I have found that a lot of praise and love, and looking them right in the eye, telling them what you want them to do for you, because they are such good boys, or girls.... worked for me. My two seem to want to do nothing, but please ol' Mom. Especially, when there is a consistant routine. It is a security thing I think, as well as knowing they are securely cared for and appreciated.
Might sound passive, but I have a very hyper 9 month Vizsla that acts like she is years older in training and all I have done is give her the look for bad and the look for love with the magic touch.Everyone remarks how controlled and well behaved my dogs are and how did I do it? I say,just like with kids, love, praise, dicipline with no harshness, and they love to please to receive more of that good stuff. If they feel insecure or alone too much, like kids, they rebel.

two times a day will help lessen the frequency of pooping i think, also remember what ed says, that puppies have to go to the bathroom after sleep, exercise and eating.

Feed the pup twice a day. When you feed the dog leave the food out for about ten minutes. If the pup doesnt eat it put it away until the next scheduled feeding. If the pup doesnt eat it when you put it out, then its not hungry. It will be hungry the next time you offer to feed it. Its important that it eats on a schedule as opposed to being fed on a schedule. If it eats on a schedule it will poop on a schedule.If it hasnt pooped when its suppose to then youll know it and then youll know to keep working at it before you put it back in the crate again or feed it again.

We're starting twice a day eating today. I just fed him at about 5:15am and the next feeding will be in 12 hours or so.

I stayed out with him until he peed AND pooped after the "go potty" command (of course, he tried to pee again about 8 more times before finally trying to poop). Then lots of praise and a treat (immediately after finishing).

I've been home with him for the last 24 hours, so it's gone well although he peed in the crate this morning (we usually take a potty break at 3 am, but apparently he woke up 5-10 min early) - my fault, though - I let him have water after 6:30, our designated stop water time for the day. I'm hoping we'll make some progress this weekend - he'll have someone here for 4 days in a row.

Well, we've made it to Sunday evening (almost 6 pm) and no poop accidents since Friday am. I've been working with him all weekend and although we've left him a few times (for up to 4 hours), he has only peed in the crate. I know this is because he just can't hold it yet, and he doesn't get scolded (never has for any accident).

We are completely switched over to all-natural kibble, and it's already making a difference. He gets fed at ~5:30 am & pm (we've never had him refuse a meal, although if he did I'd offer it again at the following mealtime) and that seems to work well. We watch his water intake as well (none after 6:30 pm) to try and minimize pee accidents.

This week will tell if things are improving - my husband will be home some tomorrow and when he's not, I will be. After that, he'll have to be left a bit more during the day. We make sure he pees and poops before any time he'll spend in the crate and we can usually get him to go (if nothing else works, we'll go for a 5-minute run and that gets things moving).