My 15" Macbook Pro retina is making a clicking/Ticking noise.

Sounds like it is the Sudden Motion Sensor.

http://support.apple.com/kb/HT1935

If you think you have a ongoing issue your best bet is to have it looked at:

Genius reservation http://www.apple.com/retail/geniusbar/

on-line https://getsupport.apple.com/GetproductgroupList.action

check warranty https://selfsolve.apple.com/agreementWarrantyDynamic.do

The retina models have an SSD and therefore no Sudden Motion Sensor. 🙂

As a few days now my MBPR is making a slight low ticking or clicking sound coming from the right side from below the right side of the keyboard. I have shut it down and closed all windows and restarted. Nothing seems to stop it. I t's happening every 10-20 seconds and only stops when I close the top portion of the screen.

There are not many moving parts in an MBPR. Where on the right side is the clicking coming from? Top rows of the keyboard, middle, bottom?

The only noise maker on a retina MBP is the fan. You might consider an appointment at an Apple store genius bar for a FREE evaluation.

Ciao.

Is there anything underneath your computer? Mine does that when I have shoved something or a pile of papers under mine. Remove the items and the clicking noise stops. It took me a while to figure that one out.

Mine started doing the same thing about a week ago. I have it connected to a Cinema display, disconnecting seems to have stopped it for now (not that that is an acceptable 'fix'), I wonder if that's the issue?

For me, the tick is coming from the back left under the keyboard by where the black exhaust vent is. I also have a SP USB3 drive plugged directly into the computer (since the display doesn't have USB3 ports).

Also it's not once every 20 seconds, it's like every other second.