It depends on what you have connected to it and which version of arduino board you are using. Sometimes that built in LED messes things up so it's best to keep it as an output if you can. I'm sure someone else has more information on when it causes problems and when it doesn't.
On the official Uno, the pin13 LED is buffered with an opamp, so you can use pin13 freely. On many boards though, the LED is just connected directly to the pin, and the load from the LED prevents it from being a useful input.
The symptom of this would be with it set as INPUT_PULLUP, the LED would light very dimly, and digitalRead() would always look low.
DrAzzy:
On the official Uno, the pin13 LED is buffered with an opamp, so you can use pin13 freely. On many boards though, the LED is just connected directly to the pin, and the load from the LED prevents it from being a useful input.
The symptom of this would be with it set as INPUT_PULLUP, the LED would light very dimly, and digitalRead() would always look low.