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I just installed a second hard drive, and I'm wondering if that voids my warranty.

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Have you read through the warranty and the manual for your Mac? It lists the user-replaceable parts as well as what is covered. Did you break anything (or add anything new that wasn't intended to be inside the Mac) is the main question on whether warranty would be excluded if you take it in for service. – bmike Jul 5 '12 at 21:30
I broke the fan connector (not being careful enough :|) so i bought a brand new one from spare parts retailer (original, apple. no difference between them). Now though the fan is 100% on all the time. Its not the fan, but the fan controller on the motherboard probably – code ninja Jul 6 '12 at 11:41
up vote 2 down vote accepted

Apple's policy has traditionally been that you can install RAM, drives and PCIe cards (on a Mac Pro), without voiding your warranty. However if there's evidence that you broke something during the install, they won't cover that, nor the 3rd party parts (naturally).

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There is no evidence I broke anything, more likely the damage is internal (inside a chip probably). No sign of physical damage to motherboard. I am taking it to apple store. Do you think they will replace it? Thanks – code ninja Jul 6 '12 at 11:42
They may ask you to put the original parts back in, but I think that's a case-by-case thing. – robmathers Jul 6 '12 at 16:38

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