How are you setting your digital pins, though the IDE or through Linux? Have you already gone through the getting started guide Getting Started with the Intel® Galileo Board on Windows* | Intel® Developer Zone ? Make sure you already have all drivers successfully installed and are using a recommended power supply.
Also, make sure you have the IOREF jumper set to the correct voltage. The IOREF is 5V and 3.3V tolerant. If your circuit is designed to one value and the jumper is placed in the other it is likely to not work. Check your connections and let me know the results.