Happens sometimes, a country that isn't one of the so-called powerhouses of world football produces a team that is way above what you would normally expect....Belgium were pretty good in Italia 90...unlucky to lose to England in the 2nd round....remember Bulgaria and Romania in USA 94?....Poland in Germany 74 and Spain 92. There are many more examples. It will be interesting to see how Belgium do in Brazil 2014.
Pretty sure most if not all left the country at a young age to train/play in places like France, Holland and Germany. So it can't be much to do with their training set up although they're obviously doing something right. Also interesting that if you look at the Belgian players in the PL, the majority their parents aren't actually Belgian. So it appears the expanse of the population because of recent immigration has had a big influence?
i think their immigration laws are quite lax and have so have a lot of french speaking african immigrants and other countries meaning they can gain citizenship and be eligible to play for the country a lot earlier than other nations.
http://www.youtube.com/watch?v=Z2t5WP1uYAI 
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Also interesting that if you look at the Belgian players in the PL, the majority their parents aren't actually Belgian. So it appears the expanse of the population because of recent immigration has had a big influence?
It appears they have invested heavily in youth football.
Maybe we should have a look at how they are doing it.