I got the guardasil shot when I was around 14, I am now 20. I have only been sexually active for a year or so and can't get aroused whatsoever even before I was sexually active. I was reading online all the bad affects people have had with the guardasil shots like infertility and I wondered if this shot could've messed up my sexual organs.

Even if it did arousal and infertility or messed up organs are two different things. You can have your uterus taken out and still be aroused. Many people are naturally not aroused. Some it could be a low libido.