Hi, I'm currently looking for a position in the game industry as a software engineer.
I have been working for 2 years on non-game software and 2 years on mobile games developing infrastructure and gameplay mechanics.

My desired position is in Graphics\Engine development but I'm lacking real experience in these areas, even though I do study these areas and do my own projects and working towards a MSc degree in that field.

When I look at company web sites I see a lot of demand for graphics programmers but I'm not sure if I currently hold the right requirements for getting such position.

On the other hand there are gameplay/tool programming positions that seems like I do qualify for.

My question is whether its OK to apply for more than one position at the same time, and if you think its not, which should I apply for? Can I apply to the graphics position and in my cover later say "hey, I'm also interested in Gameplay if you think I'm more qualified for that than Graphics" or something like that?

What would you do?

Choose one to apply for. If your application looks good for the other, they'll still want to interview you.

Most companies aren't going to hire engine or graphics programmers without experience in the field. Core mechanics are too important to give to somebody who doesn't have any demonstrable professional experience. Go for the gameplay job since that is something you have experience with. After you have had the job for a couple of months and have proved you can do your job and have gotten to know the various leads see if they have any small tasks you can do. Once you have proved you can do that see about getting a sideways promotion out of gameplay.

Can I apply to the graphics position and in my cover later say "hey, I'm also interested in Gameplay if you think I'm more qualified for that than Graphics" or something like that?

It depends on the company.

Large companies -- especially larger locations with 200+ people -- you should apply for any individual job that interests you. Two different openings may be on different teams and reviewing your information for one may not be considered for another.

Small companies -- especially small studios with 30 or fewer people -- let the HR person know you are interested in all of the jobs you qualify for.

All the places in between you need to use your judgement on. If the job advertisements are clearly within a single team at a smaller company, that's one contact. If they're larger and the ad is ambiguous for teams, and there is a good chance the studio is large enough to have multiple teams, consider multiple applications.

Thanks for the feedback, I read a post by the HR woman at Naughty Dog about them write way to apply for jobs at their studio and she clearly stated that one should not apply to multiple positions at the same time.

I wasn't sure if I should take this advice to other studios.

What I did so far was if a company asks for the CV via mail, I will apply to one position but state in the cover letter (which I try to make it as specific as I can) that I'm interested in Graphics programming, Gameplay etc.

If its a large company with multiple locations and they have their own form system, for example: Ubisoft, Rockstar, EA etc. I would apply to everything I'm interested in.

I guess I will continue with that approach.