PokéBase - Pokémon Q&A
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Sometimes when I go to battle in Pokemon Diamond/Platinum the pokeballs along the top of the DS touch screen start shaking.

Why is this?

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They shake when that pokemon is close to levelling up - I think it's when you have around 1/8 left on the EXP bar.

The six balls in order correspond to your party pokemon left-to-right, top-to-bottom if you didn't know. (Although if you switch pokemon the ordering switches too. The current battling pokemon is always #1.)

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Pokemaster is right. It is when their close to grow a level.
Source: Pokemaster & Experience
Wow...I had no idea. I just thought that when it shook that pokemon just wanted to fight. Yet again they don't have minds of thier own. I feel stupid now...
Pokemon do have minds of their own