The idea is resonance. If there is an object within your body that makes you sick, then you can destroy it with its resonance frequency so the illness should go away.
The object is called Bacteria, or Virus or maybe a Parasite.
There is also the idea of frequencies that have positive effects by itself. This is more a belief system. So that 528 Hz should be "Love" or other frequencies that shall activate "Chakras" etc.
The resonance theory is proven and works. (You can destroy these objects with frequencies).
Some other frequencies are found by practice (some people have positive effects with them, so they are using them) or by mathematics (the resonance frequency of some drugs shall do the same as the drugs itself, without the negative effects of the physical drugs ... but this is also more believing as there is any hard scientific facts of it).
For more details, please check the link: