The answer will not be known until October 2012. There is a high chance though as Annabeth and Percy are dating.
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First chapterof Mark of Athena
Yes! In the end they were thrown into the lake and they had a really sweet underwater kiss. Last chapter of The Last Olympian. (FYI, somehow even Arachne, the mother of all spiders, managed to look at this kiss and made a really nice tapestry showing it, which, unfortunately, gets destroyed in the third book of Heroes of Olympus (The Mark of Athena)......
Oh, dude, like, in the Percy Jackson book series, Annabeth and Percy kiss twice because of, like, their deep emotional connection and all that romantic stuff. It's, like, a big deal in the fandom, you know? So, yeah, they totally smooch twice in the books.
Actually in the actual movie, they didn't!! They were about to and then suddenly Annabeth takes percy's sword and says something like: "Rule number one, never let your opponent distract you!" And then they fight again and that's when the movie ends!
The Mark of Athena will be the third book in the Heroes of Olympus series by Rick Riordan, the series proceeding Percy Jackson and the Olympians. There is no mention of an actual 'Mark if Athena' in Greek Mythology. The name comes from a prophecy foretold in The Son of Neptune.