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My puppy is about 10 weeks old. I was taking him out every 3 hours at night, but my vet said that at 9 weeks I should let him go the whole night and take him out in the morning. I typically take him out at midnight and then at 7am the next morning.

He keeps peeing and sometimes pooping in the crate. Should I clean the crate right away or will he learn if I make him lay there?
 

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We never took Cali out during the night, despite her being a 2.5lb Papillon puppy. We just put her crate on my bed, made half of it newspaper and then put a toy and a blanket in the back. She did have a few accidents the first couple nights, but after that, she was fine for the night (10pm to 6am). She's now about 15 months old and never has accidents in her crates during her usual 8 hour crate times, and she now sleeps on my bed without an accident (which she's been doing since about 5 months of age). :)
 

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Make the crate smaller. It should only be big enough for the pup to stand up in and turn around. If it's bigger, it gives the pup an area to use for toileting. DON'T let him lay in pee/poo. This will undo a dog's natural instinct to keep its den clean, and will make housetraining very difficult.

What breed is your pup? Small dogs have very small bladders and often take longer to housetrain. Getting up once during the night isn't unreasonable, but your pup shouldn't need to go every 3 hours. When they're laying still in the crate, the lack of activity slows down the bladder urge a little. When you take him outside, don't have conversation, other than to tell him to "go potty". You don't want the pup to start waking up to play. After he goes, treat and praise, then return him immediately to the crate for the rest of the night.

10 weeks is very young - patience is the key.
 

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My puppy wasn't able to hold it through the night until 12 wks. We kept his crate open in an ex-pen with pads on the floor and he used those at night, but kept his crate dry. Once he stopped using them (and started shredding them instead) we took them away. After a month with no accidents overnight we transitioned him into just the crate with the door shut. It worked well for us, though I know some people may be opposed to various aspects of that plan.
 

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At 9 weeks the puppy should be let out once, maybe twice in the middle of the night if needed. Most dogs don't like to mess where they sleep, but if they have no choice they will. I had a german shepherd puppy that took 3 months to potty train, now she is fine with no accidents and out of the crate.
 

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We never took Cali out during the night, despite her being a 2.5lb Papillon puppy. We just put her crate on my bed, made half of it newspaper and then put a toy and a blanket in the back. She did have a few accidents the first couple nights, but after that, she was fine for the night (10pm to 6am). She's now about 15 months old and never has accidents in her crates during her usual 8 hour crate times, and she now sleeps on my bed without an accident (which she's been doing since about 5 months of age). :)
I'm the same with Benji although I never thought about putting the crate in the bed! I did put his litter box on it though (he came litter box trained from his breeder and its a king sized bed). The first night he got up once to use it, the second night he didn;t get up at all... Now I wake him up if/when I wake up and put him in his box, he'll use it and go back to bed! Benji is 12 weeks and 2.2lbs! As long as he goes within a few min of waking up he's usually fine to make it through the night...
 

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I'm the same with Benji although I never thought about putting the crate in the bed! I did put his litter box on it though (he came litter box trained from his breeder and its a king sized bed). The first night he got up once to use it, the second night he didn;t get up at all... Now I wake him up if/when I wake up and put him in his box, he'll use it and go back to bed! Benji is 12 weeks and 2.2lbs! As long as he goes within a few min of waking up he's usually fine to make it through the night...
It does have it's cons though.. I felt horrible one morning when I woke up to find the crate on the floor on it's side.. Cali didn't even make a fuss though or else I'd have woken up. That was when I decided to just try her sleeping on my bed.. and she did fine so that's how we've kept it. :) Just so long that she gets out as soon as I wake up, we don't have issues.. although up until recently, she'd poop when she first got up and then ten minutes later.
 

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It does have it's cons though.. I felt horrible one morning when I woke up to find the crate on the floor on it's side.. Cali didn't even make a fuss though or else I'd have woken up. That was when I decided to just try her sleeping on my bed.. and she did fine so that's how we've kept it. :) Just so long that she gets out as soon as I wake up, we don't have issues.. although up until recently, she'd poop when she first got up and then ten minutes later.
Awww poor cali! Benji would have screamed bloody murder!!!!! My bed is too high for him to jump off although last night he had to poop really bad and jumped off then cried because he couldn't get back on... I'm just glad he got off the bed to poop I couldn't even be upset that he didn't make it to the litter box... (my door was closed!)
 
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