Biophotons are photons which are emitted by plant and animal tissue, seeds, eggs and other living things. Healthy cells only produce a few biophotons a minute, making the phenomenon difficult to study, as opposed to bioluminescence which is something else altogether. Biophotons are produced when free radicals react with ATP (a cell's energy source).

Here's a detailed reason:
Ordinarily, biological chemical reactions take place in several steps with each step making efficient use of energy. However, because free radicals are so energetic they use up all the energy in one big reaction. As a result, not all of the energy is used and some is absorbed by an electron in the tissue under attack. The additional energy makes the electron unstable, and causes it to emit a photon - this emitted photon is the biophoton. Thankfully, antioxidants in the tissue generally destroy free radicals before they can react, meaning that usually few biophotons are given out. This is also the reason why healthy cells emit fewer biophotons than damaged cells.

Some biologists believe that biophotons have the potential to form a communication system inside living organisms, and as distress signals. There may also be medical applications too, for detecting damaged muscles and other parts of the body.

Researched from NewScientist article (Body Talk, issue 2331, 23 Feb 2001). And no, I didn't copy it.