It is a nightmare for every runner.
Side-stitches can ruin your whole exercise as they force you to abort your training until they decline.
Yet everybody who has already experienced side-stitches knows that they often hold on until you completely cease your training unit.
I would like to give you some advice as how to prevent them from happening in the first place.
Side-stitches have to do with your diaphragm.
In fact a stitch is nothing else but a muscle spasm in the diaphragm.
The diaphragm is a tissue of muscle between the thorax and abdomen.
It moves up and down as we breathe to reduce and expand our lounge volume.
Knowing this link between stitches and your breathing gives you an idea about the importance of proper breathing during workout.
Things you can do to prevent side-stitches:

• After eating a big meal make sure to postpone your exercise at least 2 hours.
  Having a full stomach can cause unnecessary spasms.
  
• Take long, deep breaths during your run.
  Doing the opposite will not use all your muscles to their full extent.
  Even more important is that your lounge volume will remain more or less constant when doing short, rapid breaths.
  Therefore your diaphragm will stay in a upward position also causing spasms.
  
• When running do not start to swallow your breath but try to evenly in- and exhale otherwise you are also more likely to experience spasms.
  
• Be sure to drink enough water before starting your workout as to keep the muscles hydrated and thereby reducing possible cramping.
  
• Try to warm up before you gradually speed up your run.
  If you immediately start running with maximum speed you're very likely to be taking quick and short breaths which will induce cramps.
  

I hope when you keep to these basic ideas you'll experience a pain-free, relaxing run.
Enjoy.