For two years I thought I had a gluten intolerance, however my symptoms were just not going away. I had continued negative tests for celiac disease among many other tests for several other possible problems. So one day it dawned on me eliminate Quinoa from my diet for a couple months and then try it again. When I finally did try it again, I had a day of crippling pain along with vomiting and very loose bowels. This was all within a half hour of eating the Quinoa. So I started to do some research. It turns out that the Saponin that grows on this stuff acts in me as gluten does in a celiac patient. It was creating holes in my intestinal walls (thus such horrible pain). If you do not wash quinoa properly, you can ingest the naturally occurring saponin, which protects the plant from insect and fungal attacks. Saponin is soapy, bitter, and toxic, and is actually used to make detergents. However, for those of us who are allergic to Saponin; we can wash it all we want, but there will always be traces left.
Ever since I cut Quinoa out of my diet all of my symptoms have vanished. Its a shame because I really loved the stuff. Amaranth is a great alternative if you are looking for that flavor and texture without any horrifying pain.