I'm not sure when it has been started to make clicking sounds randomly, but it has been bugging me a while. Any idea that what could be cause this problem?
I'm using MAC OS X 10.8.2 and late 2009 13 inches macbook pro.
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My guesses would be either the hard drive or the DVD drive. Your best bet is to have Apple take a look at it. You should make a genius bar appointment at the apple store nearest to you. Unfortunately if they find something wrong your machine is probably out of warranty, but at least you can get it diagnosed for free.
I have a similar model and experienced the clicking sound too. Read this: http://6ixpassions.com/post/1095520847/fix-the-ticking-clicking-sound-in-your-macbook-pro
I had this same issue after my Macbook Pro fell out of my backpack. My clicking was to the right of the trackpad. Took it to Apple and within a few minutes they diagnosed it as a hard drive error.
I went and purchased a new hard drive, backed up my data via Time Machine on external hard drive and swapped out the hard drive myself.
I have minimal tech experience but after watching a you tube video I was able to swap hard drives pretty quick.
*Make sure you keep the original hard drive. Apple said if I ever have to send my Mac in to get serviced by Apple they will require the original parts to be installed*
Hope that helps!