You mean in the TCG?
When an Active Pokémon attacks, the attack they use may specify an amount of damage to be done to the Pokémon being attacked. Damage is tallied up, by way of damage counters, in order to Knock Out an opponent's Pokémon. Each damage counter counts as 10 damage, so, for example, if a Pokémon had 120 Hit Points and had twelve or more damage counters on it, it would be Knocked Out. Damage done by attacks may also be affected by the Weakness or Resistance of the Pokémon being attacked.
http://bulbapedia.bulbagarden.net/wiki/Damage_counter#Damage
It is a little chip you put on a Pokemon to show it is damaged.