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Booklist: Male Protagonists in Teen Fiction
Melissa asked for recommendations for a 16-year-old boy, specifically realistic fiction with male protagonists. In alphabetical order by author:

Twisted by Laurie Halse Anderson
Funny Little Monkey by Andrew Auseon
Nothing but the Truth by Avi
Shift by Jennifer Bradbury
Candy by Kevin Brooks
Staying Fat for Sarah Byrnes by Chris Crutcher
Beastly by Alex Flinn
Breaking Point by Alex Flinn
As Simple as Snow by Gregory Galloway
Playing in Traffic by Gail Giles
Shattering Glass by Gail Giles
Looking for Alaska by John Green
An Abundance of Katherines by John Green
Paper Towns by John Green
Godless by Pete Hautman
Totally Joe by James Howe (Sequel to The Misfits)
Busted: Confessions of an Accidental Player by Antony John
Kimchi & Calamari by Rose Kent
Are We There Yet? by David Levithan
Boy Meets Boy by David Levithan
Wide Awake by David Levithan
Sleeping Freshmen Never Lie by David Lubar
Play Me by Laura Ruby
Drums, Girls & Dangerous Pie by Jordan Sonnenblick
Notes from the Midnight Driver by Jordan Sonnenblick
Stargirl by Jerry Spinelli
Give a Boy a Gun by Todd Strasser
The Rules of Survival by Nancy Werlin
Peeps by Scott Westerfeld
So Yesterday by Scott Westerfeld
I Am the Messenger by Marcus Zusak

Here are some of my sci-fi/fantasy favorites with teen male protags:
The Fallen by Thomas E. Sniegoski
Straight on 'til Morning by Christopher Golden
Prowlers by Christopher Golden

Two protagonists, one of each gender, split the POV in these realistic novels:

Thirteen Reasons Why by Jay Asher
Nick and Norah's Infinite Playlist by Rachel Cohn and David Levithan
Naomi and Ely's No-Kiss List by Rachel Cohn and David Levithan

Please consult my Multiple Narrators booklist for additional titles.

Two or more protagonists, at least one of each gender, in various genres:

The Subtle Knife by Philip Pullman (second in His Dark Materials trilogy, following The Golden Compass)
The Amber Spyglass by Philip Pullman (third in the trilogy)
The Misfits by James Howe (then read the sequel, Totally Joe, listed above)
The Watcher by James Howe

What about this?

The Book Thief by Markus Zusak (Death, the first-person narrator, is genderless)

I would also like to add two with female protagonists:

The Body of Evidence series by Christopher Golden and Rick Hautala - Though the main character is a teenage girl, many of the supporting characters in this intriguing murder mystery series are male, including but not limited to the medical examiner, his assistant, and one of the main detectives, not to mention Jenna's father, who is a criminology professor, and her friend Hunter. There are ten books in the series, all of which are written in third person. Start with the book Body Bags.

What Happened to Lani Garver by Carol Plum-Ucci - The title character, Lani, is the boy who befriends the main character and changes the way she views her popular friends' values and virtues (or, rather, lack thereof). This book is the anatomy of a hate crime. It is brilliant.