For once, lower quality facilities can't be singled out for this one. The ACL issue is also present at the NCAA level, where a similar number of players of both genders share the same high quality natural and/or artificial pitch at a university. Anecdotally, in my 7 year playing career I had 2 teammates do ACLs and 7-8 women. Just recalling and typing that is shocking how close it is to the stats, unfortunately.Women are 2-6 times more likely to get an ACL injury. There is a three year study looking into the reasons that started in April.
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The pitches and facilities used by women and girls teams are usually lower quality than the men's. Again this is something that's obvious even down at u8s grassroots football in my area.
The point is the science needs more work, but there are a lot of top organizations (US National Institute of Health, the PFA, Nike, Puma, etc.) investing in finding out. Hopefully the answer ends up being "buy these new boots" and not "you'll have to roll the dice with your daughter's knee if she wants to play."