If your just getting a POP like click, with no pain don't worry about it, its natural and healthy as its just a build up of nitrogen,oxygen and carbon dioxide gases in the synovial fluid due to inactivity, and the POP is just them air bubbles dissipating.

I've had this for a couple of years now - actually, only my right knee clicks when I squat or climb stairs. There's no pain at all so I haven't bothered checking it with a doctor.

Eating paleo haven't changed this and I doubt it's related to food. I would say it's not crepitus in my case, because it sounds more like a "mechanical" pop - it's probably related to cartilage.

I'm snap crackle pop in the knee area as well. Avid cyclist and CF'er, ex-competitive swimmer and have always had 'em. I found this:

http://www.mobilitywod.com/2011/06/episode-267365-mobrx-for-lound-creaky-knees.html

and it's been helpful. Just say no to Crepitus! :)

Knee-clicking can also be a related to torn cartilage, like the lateral miniscus. If you put pressure on the knee by doing a deep squat, does the clicking turn into more of a pop, or a minor knee lock? If so, you should get an MRI to diagnose the damage, which might require surgery. Probably a worst-case scenario, but I ignored this for years until the damage kept getting worse.

I'm experiencing this type of clicking too, there are a lot of things that can cause it(according to clicking knee)

Kent, i also broke my ankle once, and it makes clicks every step too. I wonder about the knees clicking tho. Maybe muscle imbalance, maybe not. It used to do that even when i was very fit and taking care muscle imbalances when i did road cycling.

I used to have this years ago. Never hurt at all, just made a clicking sound on the stairs, exactly like you say. I was going to Bikram yoga for a while and the poses where you basically stand flexing your quads and "lock your knee" as they call it helped me a lot. Don't have clicking anymore, and I haven't been to Bikram class in years either.

There are a few reasons for a clicking/popping sound.

The most common is crepitus, which typically occurs because of gas buildup in a joint. This is often not very harmful, if at all. However, it may be due to cartilage erosion.

Clicking can also occur when a tendon or ligament is snapping across a bony surface. This is not great, as the soft tissue will slowly erode over time.

Knee clicking can be due to hypermobility of the patella. A solution for this is strengthening the muscles around the kneecap. I don't know much about the anatomy, but have heard anecdotally that balanced training (for example, working the hamstrings equally) may help for some reason.

My ankle clicks with nearly every step. It's done that since I broke it 30 years ago.

My knees click when I squat. I attribute that to just getting older :)

I have always had creaky knees with various clicks and pops, especially when standing up from a sitting position. The two things that helped a lot were going Paleo and vitamin D supplements. The vitamin D especially I think had a huge impact. I started with 400IU per day, then 800IU, and today I started taking the 5000IU from iherb.com. Lots of threads here about vitamin D supplementation.

could be hip disfunction IMO. Possible lack of engagement of gluteus medius

I have been diagnosed with Chondromalatia paetella .. which essentially means my knee caps do not move properly. For years I have suffered with not being able to bend my knees properly and the pain was always worse coming DOWN stairs than going up- which is why Docs took a while to figure it out . Normal Arthritis would cause the opposite problem.. since starting CrossFit and eating Paleo .. all of my symptoms are gone. I also did do acupuncture for a year before and that helped as well. My belief is that FISH OIL and regular exercise are the key to getting rid of symptoms like these.

My knees used to click. I took some manganese supplements for awhile. The knees stopped clicking.

I have had this my whole life and it hasnt stopped even after 6 months of paleo. Could it be some sort of food intolerance issue, like from nightshades?

Your question made me just realize that since going paleo a little over a month ago, mine have stopped doing that.