Foot pain can be from conditions affecting the skin, muscles, tendons, ligaments, joints, nerves, bones and much more! If an x-ray doesn't show anything out of sorts, it is likely that the condition is not bony - as x-rays only show bone. If pain is severe enough or if there has been an injury, your doctor may opt to order a diagnostic ultrasound or MRI.  Both of these types of imaging offer the ability to look at soft tissue (ie. anything that ISN'T bone).