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My wife and I got a 10 week old Irish setter puppy a few days ago. We wanted to crate train her and have had mixed results.
Anytime we put her in the crate and close the door she cries until she tires herself out and sleeps. The first night was the worst, it has gotten a little better but she still cries herself to sleep each time. We keep her crate in our laundry room gated off but she will NOT tolerate being in that room by herself with the gate closed either. She spent 25 minutes crying, and jumping into the gate and walls. In the crate is better.

Background:
1. We have her on a consistent schedule of play, sleep, and potty breaks throughout the day making sure to tire her out before bed, she is usually complete wiped out by bedtime at 11:00. I wake up around 2:00 (or when she whines) to let her potty. She hasn't had any accidents in her crate at night. I don't mind getting up to take her out while she is so young.
2. During the day I take her to my healthcare office where she socializes with my staff, and hopefully one day with patients too. Her schedule it still kept but when it's time for her nap I put her in her crate in her area in the basement, I can't keep her in my personal office because of her crate crying and I move between my office and treatment rooms throughout the day so she can't be near me all the time.
3. We got her used to her crate with treats, she will readily go in the crate, and we exclusively feed her in the crate but she cries soon after closing the door.
4. Last night (night 4) I slept next her crate until she fell asleep, still cried herself to sleep.

Ours goals are to raise an well adjusted independent family/hunting and possibly therapy dog.

We are worried she won't be independent and that she will develop separation anxiety or something else.
Her most comfortable spot is on a rug in our living room, it's the first spot she laid on when she brought her home. We are hoping she will get better in the next 1-2 weeks but we're worried she may develop unhealthy habits. We appreciate any suggestions
 

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Poor baby. Taken from her family and litter mates bought home and then (in her eyes) abandoned forever in isolation.
A crate should be a safe place not a punishment or a place of fear and at the moment thats obviously how she views it. You are with her then she goes in the crate and you leave her alone.. I know you said you slept by the crate once but the rest of the times she is alone.
Ive never used a crate but my dogs know when the lights go out they go to bed and stay there unless they are ill or there is a threat then they alert us.
I think if you continue down this path of shutting her away from you there is far more likelyhood of her developing issues that if you allow her to be near you. Some people put the crate next to their bed and gradually move it further away until the dog feels happy that it is a safe place. Many add a sweaty sock or tshirt so the pup feels close to your scent. Maybe try that if you are going to go down the crate path..
 

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Discussion Starter #3
Thank you for the response. My thinking was that a calm, quiet place would be better, especially long term. In the past, puppies that I have been around would cry the first night or two but then be ok. I put 2 shirts in her crate, one that each of us wore; it does seem to have helped. Unfortunately her being happy in her crate is a necessity due to eventually taking her to our cabin and other family members homes where other dogs are present or not allowed in parts of the home.
I will try keeping her in her crate in our room for now. I hope it goes well.
 
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