There are many molecular targets for Low Level Light Therapy (LLLT). The chief target appears to be cytochrome C oxidase in mitochondria, which then initiates a cascade of molecular events that signal the cell to perform various functions. Although visible light can produce photochemistry, infrared radiation only produces molecular rotations and vibrations. A probable explanation of how 633 nm radiation can produce the same biological effect as 904 nm radiation will be presented. The light activation of enzymes by multiple mechanisms will be discussed. To further enhance the scientific basis of LLLT, I propose that gene array experiments be performed at the wavelengths that have been shown to be most effective for different therapies with LLLT. Then we will know what genes are activated by the different wavelengths, and therapy can then be designed with greater confidence for success. It will also help us to determine if the use of more than one wavelength in a therapy might be advantageous. Think of the different wavelengths of light as different drugs, therefore it is important to determine which drug is best, and also the optimum dose.