Is there a way to check for this other than brain scans? My son is incredibly clumsy at 2.5years old and he fell off the bed when he was younger, perhaps 1 year old, and had a nasty bang to his fore head. He is a twin and his sister doesn't have as many falls as he does.
I wouldn't worry too much. I was very late learning to walk among other things and a doctor told my mom that I was "not exactly gonna be playing outfield for the Yankees". No Yankees yet but I ended up an all-state athlete, plus a two-sport college athlete. Most days I'm not totally stupid either.
Boys will be boys. I fell out of my bed at the age of 8! As far as I can tell, I am perfectly normal with excellent sense of balance now at the age of 30. As long as your son eats well, sleeps well, and is otherwise healthy, give it a few more years before you really start to worry.
Also, make sure to encourage movement (adults call it exercise, for kids is play). I used to be really clumsy as a kid before I got into sports as a late teenager.
Consider occupational therapy as well. It was very very helpful for my daughter, who was "behind the curve" with her gross motor skills. It's not just about increasing physical ability, either. Lack of core strength can affect the ability to sit still and focus as the body gets fatigued more easily.
Something tells me that going to your family doctor and saying 'I'm concerned that my son is missing some of his brain' isn't going to get you a referral to radiology, but who knows. If he hit his forehead really hard I'd probably take him in in case of a concussion, and that would probably tell you in some detail.
My 9 month old had his brain (and other organs) checked whilst in the womb during one of our ultra sound checks. BTW, it might be a country specific thing. I'm in the UK.
This is very unlikely to be the cause. If you're really worried about his clumsiness, I'd see a doctor -- there are lots of more common causes, many of them not even serious.
