I have decided to start the Pauling regimen but want to know if there are any known side effects?
As we try to point out in the book, http://practicingmedicinewithoutalicense.com/, any "side effects" are generally from not dosing high enough, i.e. not taking an optimum amount of vitamin C and lysine.
The side effect from not following Pauling's advise is heart disease.
But to answer your question, both substances have no measurable toxic dosage (you cannot kill a laboratory animal with either vitamin C or lysine), both substances are required for life in some smaller amount (vitamin C 10 mg, lysine 1000 mg) and other than a questionable report of elevated cholesterol in an animal experiment, there are no known adverse side effects to Linus Pauling's heart therapy, other than diarrhea if you take too much vitamin C at one time.
Take a look at this starting protocol, because some people are limited by how much they can take orally - let us know your bowel tolerance, and we can recommend some products.