Here's what Cordain's has to say about quinoa:
I believe it is in the same family as spinach and technically not a grain."Quinoa and amaranth are grain-like crops with potential harmful substances namely saponins. Saponins have been demonstrated to increase intestinal permeability which is one of the factors contributing to many autoimmune diseases, as well as irritable bowel syndrome. So, we recommend to avoid quinoa and amaranth, specially if you suffer from an autoimmune disease."