I'm OP in Minecraft yet i can't do any commands?

In the chat it say [Server Opped: (my username)] Yet when I try to do any commands it says that i don't have permission to do this command.

If the server is vanilla (meaning no mods or plugins, such as Bukkit) and it's your server, check your op-permission level. You'll find this in the server.properties file by opening it with Notepad.

There are four levels.
1) Able to bypass spawn protection.
2) Able to use /clear, /difficulty, /effect, /gamemode, /gamerule, /give, /tp in addition to editing command blocks.
3) Able to use /ban, /deop, /op and /kick.
4) Able to use /stop.

Op permissions apply to *all* ops in that server, so having it set to 2 won't allow you to spawn in items or give anyone items, while 3 will.