Mainboard doesn't recognize 3.5 SATA hard disk drives

Hello,
Tried two 3.5 SATA HDD (80GB and 500GB) and neither of them worked, but they work well in USB enclosures. These hard drives do not show up in the BIOS of that particular machine. Interesting thing is that 2.5" HDD drives work perfectly, they show up in BIOS and OS boots up without any problems. I already tried different SATA cables, different: SATA slots, SATA power connectors. Does anyone had similar issues and know how to deal with it? Hiren's CD didn't work because HDD not being found while connected via USB or SATA.

You don't define sata model of any hardware, are the drives sata2 or sata1, same for the motherboard controller. If your trying to initilize in achi mode you need drivers first.
Most sata drives have a jumper setting if you need to configure as sata 1, the controller cannot change upwards if it's sata1 but jumping the drives down to sata1 will work if that's the case.
As you probobly know setting the controller sata mode to ide should work for initializing new drives without any additional drivers.

In your post I see loads of misleading information. SATA2 is backwards compatible with SATA1 and you don't really need to play with jumpers. As I mentioned before, my other 500GB 2.5" factor SATA drive (WD caviar blue) works fine (I even tried with my older 120GB 2.5 SAMSUNG), computer passes POST screen and I am able to access BIOS SETUP. AHCI drivers aren't important at this stage. It's complicated and I would appreciate only answers and possible help from the guy who knows what he's talking about.

What is the motherboard you are using?

Very old post (yes I know, flame away) but as it was one of the first Googled results I found, I imagine others will come here looking for the same solution.

Roonj was exactly right. While SATA is indeed backwards compatible, many older motherboards aren't able to automatically negotiate with the SATA hard drive to bring it down to a speed it can use. Placing a jumper in the right spot (usually 1-2, though check your HDD manufacturer's web site for their placement) will force the hard drive down to 1.5 (aka SATA I).

I had the exact same problem today. Tested it 9 other SATA hard drives before I noticed the correlation that the mobo wouldn't identify faster hard drives. With the jumper, all 9 are detected just fine.