My Life as a Human Hairball by Bill Myers

Just when you're sure Wally has bungled through every misadventure imaginable, this nerdy kid stumbles, staggers, and k-splats his way smack dab into a brand new frontier - the human body. When he and Wall Street, his best friend (even if she is a girl), visit a local laboratory, they are accidentally miniaturized and swallowed by some unknown stranger. It is a race against the clock (let alone Wally's own klutzoidness) as they fly through various parts of the body - from the stomach to the blood system to the brain to the eye - in a desperate search for a way out while all the time learning how "fearfully and wonderfully we are made."