I'm 161 cm and weigh about 48 kg. I have had my period regularly the last 6-7 years. But the last six months i've barely had it at all. It disappeard after 4 months of really hard training. I have lost some bodyfat, but gained weight (probably because of muscle mas). I have a body fat percent around 10-11, but don't want it to be higher. Anyway, I know the loss of mye period is not a good sign, what can I do to get it back without gaining fat? And what might happen if it doesn't come back?
I highlighted the problem. That's a too low body fat %, for sure. Men can go to 10%, but women can't (or can, but shouldn't as it is seriously unhealthy).
What you are experiencing is part of what is commonly called the "athlete's triad": an eating disorder, amenorrhea (loss of period) and low bone density. See more info here:
http://en.wikipedia.org/wiki/Female_athlete_triadWhichever role sports and fitness play in your life, there is NO reason to have the athlete's triad. If you are into fitness for a living (say, you are a personal trainer, or a professional athlete), you should gain some bodyfat. You should have access to a nutrition in your gym -- talk to him/her.
If you are into fitness for health reasons (say, you were overweight and started working out to lose excess fat), you overdid it, and you'll face health problems from being underweight which have similar or greater risks than if you were overweight. Therefore, for health reasons, you should gain some fat.
If you are into fitness for aesthetic purposes (my suspicion, given your age and extreme concern over body fat %), you'll have to take this VERY SERIOUSLY. I have a sister who has an eating disorder, and it's no fun. My advice is to seek professional medical help NOW. Go see a general practice doctor for a general check-up, and ask him/her whether he/she thinks you should see a nutritionist and/or a psychologist. That doctor should check you for several indications including your sexual hormones, iron levels, etc. Loss of the period usually indicates a non-trivial malnutrition, which might have had other effects on your body.
As for the loss of period itself: once you gain some body fat back, it should come back, and as long as you keep your body fat levels within normal values you should experience no long-term effects of this. HOWEVER, keeping your body fat this low at this critical stage of your life (when your bones are getting stronger) will put you at a much higher risk of having bone problems later, such as osteoporosis in your early 30s (which for healthy women isn't a problem until after menopause, if ever).
By the way, a question (only answer if you are comfortable): why do you want to keep your body fat at such a low level? Let me tell you right away that you'll look much better to us men if you are at a higher value.