Discuss with the shy teenager what kind of feelings that he's encountering. Even though the person may be shy, he may be perfectly fine with that. Another group of shy teenagers might have accepted him as well.
Help your teenager overcome her shyness by having her volunteer her time at a some institute or office. If she's in a surrounding without many peers, she can speak up a bit more and get to know people on a more personal level.
Ask your shy teenager if he would like to invite a person over the house for dinner one night. While he may feel awkward about doing so, it may be a good idea to break social barriers that he feels at school with so many of his peers around.
Encourage your shy teenager to join one group at school that fits her personality and talents. By showing off her special knowledge or gifts amongst her peers in a small group, she may surprise some people and make new friends.
Talk to your shy teenager about his self-esteem issues. If he's fine with how he is, then he may not need counseling. If he's very down and experiencing depression or anxiety, counseling may be necessary to remedy the problem.