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I'm trying to find the title of a CYOA (or variant series) book, that centered around the main character being shrunk down in size and traveling through the human body, fighting blood cells, etc. It was very similar to the movie Inner Space, but definitely a choose your own adventure story. I remember reading it as a kid but can't for the life of me remember the title so I can find it again.

Any help would be appreciated! 

Sounds like "Fantastic Voyage the CYOA"

The only books I found in the official CYOA line were "Help! You're Shrinking" and "You are Microscopic.' There was another one "Prisoner of the Ant People" but none of them involved what you're talking about.

Might have been from another series. (Which Way Books perhaps)

Yes, very much like the Fantastic Voyage. I checked out those three but none of them seemed correct either. I really do believe it's from another series. I've checked Which Way and Twist-a-Plot, but neither seem correct either. 

In case anyone else is wondering after stumbling across this post, I finally after searching for months and years found the book title and series. It was a scholastic series called Explorer. The one I was searching for is called Destination Brain by Seth McEvoy.

I found this one called MY PEN PAL IS A ZOMBIE 

That's great I'm very happy for you but maybe we don't need to bump an eight month old thread about a completely different book to announce that.

I read this post wrong...oops :p