The present work is a review of the most potent allergenic proteins of legume seeds, mainly soybean, pea seeds, and peanuts. It emphasises the importance of cross-reactivity between proteins of particular seeds and nuts. In the paper, there are discussed some discrepancies in the results reported on the most allergenic protein fractions occurring in particular seeds, as well as threats emerging from ambiguous results to some atopic patient population. The problem connected with more and more common consumption of genetically modified foods is also approached in the present work.