Do you by chance have the FTDI programming board plugged in while you're doing this?
I ask because it will interfere with any other uses of the serial port. This is why people often use softwareserial on 2 and 3, to keep clear of the hardware serial port on 0 and 1.
If you're writing a sketch that e.g. sends a test pattern out the serial port, and are running it on battery without the FTDI plugged in, that's the right way to do it and to the best of my knowledge it should be working.