The Shadow Children Series by Margaret Peterson Haddix

There are seven books in this children's series written between 1998 and 2006. They are set in a futuristic time when no family is allowed to have more than two children.  Luke is introduced in the first book of the series, Among the Hidden, as a thirteen-year-old who has been hidden away all his life. In the first book, he meets another third child, Jen, whose dedication and sacrifice show him that one person can make a difference. For more information on the other books in the series, see the author's website.