We reviewed OS X Mountain Lion’s Messages when it first debuted its Beta version, and at that time, one of its noteworthy features (which we duly noted) was the chat history. For those of you who forget what you were talking about yesterday, chat history lets you keep every one of those conversations forever. Regardless of whether you were discussing ways to hack into top secret government files and change your name to James Bond, or just trying to decide where to eat, those conversations will be saved. The slight problem here is, while some conversations should be saved for future reference, others should be wiped off the face of the earth (or atleast your Mac), and Messages has no way to delete your chat history. It doesn’t even have a help topic on deleting chat history, so it is safe to assume there is no button or menu that can do it. That doesn’t mean it’s impossible, it just needs to be done manually.
One of the main reasons that you can’t find your chat history is that it isn’t saved to Messages in Library. On the contrary, it goes to a folder named iChat, which you will find in your Documents folder.
The iChat folder has several sub-folders, each named by date. Inside these sub-folders, your chat history is saved by name of the person you had the conversation with. You can selectively delete the entire conversation you had with anyone, and that is all it takes to get rid of your chat history. For permanent deletion, make sure you remove them from Trash as well.
Why is Messages saving chat history to a folder called iChat when it is has otherwise killed all traces of the said app? We can only guess, but we may never know (or we might, eventually).