My ds, just 3, has also been referred as he is very small for his age - always been on the 0.4 centile.
The consultant told us that as he has stuck rigidly to his centile line it was unlikely he had any growth hormone deficiency (children with GH deficiency tend to start dropping height centiles around 6 months of age when GH starts kicking in - prior to that growth comes from pre-natal hormones still in their system). A blood test confirmed this he was not deficient.
The consultant also said the most likely explanation was that his bone age was delayed. This is not considered a growth 'problem' as such, just a particular growth pattern. An x-ray of his wrist showed his bone age was delayed by over a year - in other words his bones are at the stage of development you would expect in a child of almost 2, rather than a just 3 year old. So he is now measured against his bone age rather than his birth age - and as a result is now just below the 50th centile!
Children with delayed bone age typically go through childhood being much shorter than their peers (the bone age delay tends to increase until their teens - so at 12 he could possibly be the height of a 9 year old). They also tend to hit puberty later than their peers. However the good news is that once they have hit puberty they experience the growth spurts that would be expected, and continue growing often several years after their peers have stopped - even into early twenties. So they eventually reach 'normal' height.
This growth pattern tends to run in families - although not in our case (several of you have said they or their siblings were short children but had huge growth spurts in their teens and grew to over 6 feet!).
So basically the message is not to worry, look at the pattern in your own family, and if in doubt get referred for a very quick and easy x-ray.
Obviously I wish ds didn't have this growth pattern - it won't be much fun for him being so much shorter than his peers, particulalry during the teenage years and I worry about him being bullied etc. but kids can get bullied about almost anything- we just have to make sure he has the confidence and personality to cope with being short.
Hope this helps!