Empress thank you for sharing that with me, the fact that your Dad reacted as my 'D' H did and then you didn't say anything for 6 more years terrifies me. That is the last thing that I want my dd to do while she deals with her feelings. In 15 years of marriage I never considered for one moment that he would ever react like he did.
I do think it may be, like your Dad, down to fear and not really understanding (not that I do either, but I am really trying) so I have printed off some of the links from this thread for him and given him the PFLAG number. He is refusing to talk about it just now, which is no bad thing at this point, hopefully he will come around in the next few weeks, if not I will have some very difficult decisions to make 
Mad thank you for your thoughts, I think if this had been about a crush on one girl then I would probably not have gone to the school for help, from what she says this has been a feeling she has had for a long time, she has had crushes on girls before, but even when she hasn't, she hasn't felt the same way as her classmates, for example she doesn't look at boybands and want to talk about who is the cutest etc because it doesn't feel right to her, she can't fully articulate it yet other than to say she knows she feels different, and I don't want to push her into talking about things she may feel uncomfortable discussing with me (and I have told her and the guidance teacher at school that, as long as it isn't anything I absolutely have to know about, that neither of them need to discuss their talks with me) but this is, at this point, about more than having a crush on one girl .
It is very possible that she could tell me that she likes boys next week, next month or next year, but, for now, this is how she feels and I have to be supportive. We have also had talks about the possibility of feeling different ways in the future, she may begin to like boys, she may not and she may like girls and boys, but she knows that she can come to me at any time and talk about it.
Lilka thank you, I have so much issue with what he said, even when he said that it's my fault, the word 'fault' makes it sound like something to be ashamed of, not much wonder my poor dd is struggling. I just told her that her Dad is a bit scared because it's all new to him as well and his reaction was a bit silly, she pretty much rolled her eyes, said it was fine because this time last week she was scared too, and then got on with talking about this project she is doing with the school (she is so excited about it). Thankfully he is working away a lot over the next couple of weeks so he can deal with his feelings without bringing dd down.
When I was 9, I felt different. I didn't realise why until later because I never heard the word 'lesbian' and had no idea what my feelings meant or were, and so I couldn't say 'I'm a lesbian' until I was about 13, but oh yes, I was gay at 9.
This ^ is almost exactly how dd describes her feelings, the only difference is that she does know what a lesbian is, over and over again she says she is different, even though she can't fully explain why. It's really upsetting that she is automatically seeing 'different' as 'bad' just now, but she is getting there slowly.
Pendeen I am fully aware that she is 9 and only a child, what is the magical age that I should start taking her feelings seriously? If you read my posts I haven't 'labelled' her as anything, I am just trying to support my dd with how she feels now would you really ignore a 9 year old child emotionally struggling with something until they reach an age where you decide they can be taken seriously. And I fully agree with what Empress and Lilka said too.
Daykin I am so sorry your Mum treated you like that, my Mother did the same throughout my childhood, and you're right, it does suck, I hope things are a bit better for you now 