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Help my 5.5 month old mini lop!!!

We got our first two bunnies this summer, one is a male born 5/16 and one is a female born 6/18. The male has been full grown for over a month now and has always been super healthy looking and vibrant and active. The female has never been healthy. Both came from the same breeder. Our female we got at 8 weeks old and has been housed with the older male whom adores her. About a month after we got her, when we went out to feed her one day she could not lift her head up. We researched and found she must have head down syndrome. We spent 10 days giving her water with a syringe and finally she got enough strength and resumed control of her head. Since then her eyes have been red and swollen. She is very small, being almost 6 months old now she should be the size of our male who is 4 weeks older but she's not even close. Somedays she can hardly hop around, she acts like her back is broken, but other says she's seemingly fine. Some days she has no energy and lays around. Our male is always the same, always peppy :) We recently seperated the bunnies and it's amazing how small she is in comparison and its like she's just not thriving. I have no idea what's wrong and don't know how to help her. I keep thinking she's going to get healthy but here we are now at 6 months of life and she still have swollen red eyes and is tiny. Any ideas? Advice? Please help!!!!!
 
We got our first two bunnies this summer, one is a male born 5/16 and one is a female born 6/18. The male has been full grown for over a month now and has always been super healthy looking and vibrant and active. The female has never been healthy. Both came from the same breeder. Our female we got at 8 weeks old and has been housed with the older male whom adores her. About a month after we got her, when we went out to feed her one day she could not lift her head up. We researched and found she must have head down syndrome. We spent 10 days giving her water with a syringe and finally she got enough strength and resumed control of her head. Since then her eyes have been red and swollen. She is very small, being almost 6 months old now she should be the size of our male who is 4 weeks older but she's not even close. Somedays she can hardly hop around, she acts like her back is broken, but other says she's seemingly fine. Some days she has no energy and lays around. Our male is always the same, always peppy :) We recently seperated the bunnies and it's amazing how small she is in comparison and its like she's just not thriving. I have no idea what's wrong and don't know how to help her. I keep thinking she's going to get healthy but here we are now at 6 months of life and she still have swollen red eyes and is tiny. Any ideas? Advice? Please help!!!!!

Have you taken her to a Vet ? That is the most important thing.

It sounds as though Encephalitizoon Cuniculi (EC) might be a possibility

http://www.gwexotics.com/wccms-resources/a/5/0/e/77554b90-a660-11e0-a685-0050568626ea.pdf

But only an examination by a Vet will establish a diagnosis so please do not delay getting a Vet to see her.
 
We got our first two bunnies this summer, one is a male born 5/16 and one is a female born 6/18. The male has been full grown for over a month now and has always been super healthy looking and vibrant and active. The female has never been healthy. Both came from the same breeder. Our female we got at 8 weeks old and has been housed with the older male whom adores her. About a month after we got her, when we went out to feed her one day she could not lift her head up. We researched and found she must have head down syndrome. We spent 10 days giving her water with a syringe and finally she got enough strength and resumed control of her head. Since then her eyes have been red and swollen. She is very small, being almost 6 months old now she should be the size of our male who is 4 weeks older but she's not even close. Somedays she can hardly hop around, she acts like her back is broken, but other says she's seemingly fine. Some days she has no energy and lays around. Our male is always the same, always peppy :) We recently seperated the bunnies and it's amazing how small she is in comparison and its like she's just not thriving. I have no idea what's wrong and don't know how to help her. I keep thinking she's going to get healthy but here we are now at 6 months of life and she still have swollen red eyes and is tiny. Any ideas? Advice? Please help!!!!!

What you are describing sounds too complex for us to make a diagnosis over the Internet.

In all fairness to her, you should take her to see a good vet who is experienced with rabbits. Any other vet is likely to be a flummoxed as you are by the situation.

Let us know how you get on. Do post again asking for a 'Rabbit Savvy' vet in your area if you feel you don't have one currently.

Have either of them been neutered or vaccinated?
 
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