Described herein are methods and apparatus for treating fungal nail infections and similar diseases with light therapy. In one embodiment, an apparatus that utilizes one or more blue light emitting diodes (LED) to irradiate fungus residing under and around the nail is applied externally to a toe or finger in order to kill the fungus and restore normal nail growth. Light therapy may applied in this manner periodically at scheduled times. Another embodiment involves the use of a bootie-like structure having blue light emitting diodes for irradiating the toes, heal, and foot bottom.