Applying for internship in the US as a European Student My question is about applying for a US internship(4 scale GPA) as a European student(with 10 scale GPA). 

I took a look at this thread. An answer mentions that 93% of grades are 'A's, thus leading to a 4.0 scale GPA. In my country, the average GPA in my school is 6.3/10, which depends on lots of factors (difficult exams, professor unwilling to help etc). Practically, students scoring A's (10/10 or 9/10) in courses are very limited and in some courses like Calculus non-existent.

I've seen many internship programs from large corporations where they require a GPA of 3.5 and above.

When only one student in the history of my school has scored 3.9/4.0 (converted to 4 scale from 10 scale system, 9.9/10 in 10 scale) only 1% every year graduate with 3.5/4.0 and above GPA, what are my chances of being accepted at a US program even with experience in my area of interest? Are European GPA's handled differently than US GPA's? I believe a direct comparison between the two is impossible since in reality they are two different grading systems.
As has been said, your last sentence hits the mark - a direct comparison is impossible.  I would argue that it isn't necessary, either.

I am a US native.  I am currently working an internship in the United States at a child company of a larger pharmaceutical business.  I know that my company had a "minimum" GPA for the application, but this was never mentioned in the interviewing process.  To me this implies that companies use GPA to see if a candidate meets a satisfactory minimum - it's a way to weed out applicants they know they don't want or need.  I think if you explain that your GPA is good by European standards, if indeed it is, then your application will be strong.

A few of my fellow interns are from Germany.  I don't know them well but I mention this to show that success is possible and that some companies in the United States, at least, have a good grasp of how grading scales work in Europe.  I think it worth mentioning that Europe seems to have a relatively smaller amount of grade inflation as compared to here.  That's an important point - grades are somewhat inflated here, and a 3.5 GPA probably indicates a level of performance that is different than you imagine.  Given this, I would say your chances of getting a job are good, especially if you adopt the normal tactics of applying to many positions and being prepared to take a few rejections.