Does it matter where the injection sight is for childhood vaccines?

My six year old just got Hep A and Chicken Pox vaccines at his doctor. I read on the online pages that the injection sight is usually in the arm. His pedi's asst. gave the injections in the upper thight (side). Is that Ok? He also has Aspergers Syndrome (high functioning autism), do you think these vaccines make it worse? Are they even safe?

This is a normal injection site, this type of injection is call "IM" or inter-muscular. Sometimes when the patient is young or has thin arms its a better bet to do it in the thigh where there is more muscle.
i don't think the vaccines make it worse but he would be fine with out them. Chicken Pox isn't life threatening and Hep A is very rare in the USA.

No, he'll get over it. Go see a specialist if it helps.

Yes, it does, especially for girls! It is advisable to have them on that part of the body which may not be exposed! Anyway, trust and follow the professional advice!

While these vaccines may be given in the arm, for your son I think the assistant made the right choice. Typically in the office I work at we will give injections in the leg to children who have very small arms (and a lot of 6 year olds do) or children who are very uncooperative. The reason this site works better for children who aren't cooperative is that the muscle site is bigger and that its typically easier to restrain a leg than an arm. Whoever posted that the injections are IM was only partly correct. The recommended route of administration of the chicken pox vaccine is SQ (in the "fat").
As for these vaccines making his Asberger's worse, there hasn't been any verifiable link between vaccines and ASD (autism spectrum disorders). However, if he experiences side effects from the injection like fever, its likely that it could make his behavior worse for the few days following the injections.
As far as being safe, they are. These diseases are both common (hepatitis A outbreaks can occur anywhere, but the US southwest has a high incidence) and easily transmitted. Both diseases can be fatal, although neither commonly results in death. While there are side effects and catastophic consequences possible from any vaccine, he is much more likely to experience an adverse outcome if he contracts the disease.
Anyhow, you really should check with your doctor if you have serious concerns about his immunizations. Doctors can give you _reliable_ sources of information and should have supplied you with a Vaccine Information Statement (VIS) prior to administering any vaccine. This sheet tells you what the disease is, who needs the vaccine and possible side effects or reactions that could occur.