This might be a very simple question, or it might be mistake by me
I have pin 13 set as a output and this s connected to the base of a TIP31 transistor , this then powers a 1wat LED. The thing is when i plug pin 13 to the curcit the on board LED goes out. I assume it's meant to stay on? the curcit seems to work but i wanted to check this before going any further. Thanks 
Is it completely out, or just very dim?
My initial reaction to your question was that it was normal for the onboard LED to not light when there was something else attached to pin 13, but I quickly wired it up and ran a pin 13 blinky to check. It looks to me like the onboard LED lights dimly when there is something else attached. I wonder if maybe the brightness of the onboard LED is inversely related to the total load being driven by pin 13.
Yeah. no idea, it goes out completely or almost. I was hoping to be told it's normal as the 1 watt led works fine. But don't want to damage anything ...mmm
Do you have a series resistor between pin 13 and the base of your transistor? If not you are effectivly shorting out the pin and probably drawing more then the maximum rated pin current. Damage will soon follow if not already.
Lefty
eerr . no. dam ahh bloody hell.. well it does all still seem to be working . Fingers crossed. what value would you suggest?
and thanks 
I think you are probably fine, but it would be easy enough to wire up a circuit in which you could add more LEDs in parallel and observe the behaviour of the onboard LED as you increase the load.
Just connect the supply rail of a breadboard to 13 and the adjacent ground rail to ground. Set pin 13 to blinking. Add leds mid blink and watch what happens to your onboard LED
R=V/I
eerr . no. dam ahh bloody hell.. well it does all still seem to be working . Fingers crossed. what value would you suggest?
500 ohms should be fine. Just don't wait and don't use it until you get the resistor installed. The transistor base emitter junction doesn't care that much too much current is flowing and will operate, but your poor Arduino output pin is screaming with pain and may soon perish from this earth. It's ok a standard 328 dip packaged replacement processor chip with installed bootloader can be had for around $6+ s/h.
Lefty
Yeah it's a good job there cheep. I can see me getting through a few while i make a few mistakes..duh. now to fine some resistors. Thanks for the help
I think you are probably fine, but it would be easy enough to wire up a circuit in which you could add more LEDs in parallel and observe the behaviour of the onboard LED as you increase the load.
Just connect the supply rail of a breadboard to 13 and the adjacent ground rail to ground. Set pin 13 to blinking. Add leds mid blink and watch what happens to your onboard LED
Sir, no offence or flame intended, but you seem to have just enough electronic knowledge to be dangerous. Normally I wouldn't care, but as you are attempting to give advice to others, it does bother me a little. Do you understand the output current limits for an Arduino output pin? Do you know how one prevents from drawing too much current from a output pin? Your advice seems rather unknowledgeable of this subject.
Again sorry if you take this the wrong way.
Lefty
works a treat.. nice one guy's
needels to say i went with your advice retolefty