1. Gout (probably not without large concurrent fructose intake)
2. Inflammatory amino acids (methionine...but probably not because of immediate onset of pain)
3. Allergic reaction to a protein (probably not, as very few people are truly allergic to beef protein, fish protein, etc)
4. Unrelated to nutrition- if the initial "attack" was concurrent with eating something, your brain can and will use that against you in Pavlovian fashion. Future intake of similar foods may produce the same pain signal.
5. Nitrates (probably not, as I don't imagine you're eating large amounts of cured meats)
6. House, MD (meaning...there may be a crazier explanation at play here. For example, maybe meat upset your tummy at some point, you had a crazy gut bacteria reaction, blah blah)

Solutions? #paleo

Try isolating the variables. Have protein powder isolate to see if it the protein at fault or something else in the food. Try meat fat (e.g. lard) to see if it produces symptoms. Try fasting for a day to see if it's food related at all. Heck, even try some soy protein isolate to see what that does. Obviously, don't hesitate to go to a doctor if it gets bad. Report back!

I think you should see a doctor to rule out things like Lymes disease or something autoimmune. A good GP could probably handle it but you could also go to a rheumatologist.

It seems unlikely to be related to protein in general since you say you aren't having much protein now.... It might help if you provided a lot more detail here - like is the problem related to specific proteins or just any protein, how much protein and what kind were you eating before, etc.

Shauna - any updates on your status? what have you tried? what has been the result? i'm 10 months into a process of improving my diet, last 90 days have been substantially paleo, and last 3 weeks substantially ketogenic (approx 6% cal from carbs, 61% from fat, 33% from protein). eating 1.25g protein per pound body weight. i'm an avid cross fitter but joint pain started about a month ago and it seems to be progressing (knees, now shoulders, and into elbow). i'm pretty fit for a 56 year old (13% body fat, & good strength, metcon, and speed) and don't want to think that i'm getting stopped in my tracks by arthritis or something like that. i hope to heck that my diet experimentation is the cause of my problems as opposed to soemthing i CAN'T control. so, how are you doing in your quest? thanks.

My joints ached too. And my left knee sounds like someone ripping velcro when I squat now!

(Maybe too many purines?) Gout?

Iron overload can cause joint pain. http://en.m.wikipedia.org/wiki/Iron_overload

You may want to look into the type of protein you are eating. The paleo diet cleans out your system and your body may be more sensitive to things you are eating that contain toxins. For example commercial non organic chicken has Arsenic added to it, and beef has crap like hormones and antibiotics that your system may be more sensitive to now.

I have had a similar problem that comes and goes and I am trying to figure out what is may be. I do not eat commercial meat, but I do eat fish, so maybe something in that.