The Uglies Series, by Scott Westerfield

Tally Youngblood is an Ugly in a world of Pretties. She is a tricky Ugly, one who sneaks across the river at night even though Uglies aren't allowed to. When her best friend, Peris, gets the operation that makes you pretty on your 16th birthday she feels abandoned. So when she meets another tricky Ugly named Shay they become best friends.
It all goes downhill from there when the night before the operation Shay runs away and leaves Tally direction on how to get to The Smoke, a community of runaways who didn't want to be pretty. Tally doesn't understand this since it's her life's dream to be pretty. The day of the operation Tally gets called into Special Circumstances and embarks on a long journey that ends in her finding out the biggest secret of all time.