Yes legumes may contain several anti-nutritional factors. The three main factors are:

- phasine, a protein that has a serious effect on the small intestine in some people. However, this protein is destroyed by cooking, so only raw beans pose a risk regarding its presence. Phasine though is destroyed only after a lengthy period of boiling the legume, and not by drying. Outbreaks of phasine poisoning are very rare.

- trypsin inhibitors, several of which are found in legumes. These are proteins that block the digestive enzyme trypsin; some of these inhibitors are heat resistant. The activity of these inhibitors impairs the digestion of proteins, which are thus not digested and absorbed. These trypsin inhibitors may result in malnutrition, especially in low-protein diets.

- phytates, or phytic acids, which are affected by heating, but require other processing (such as fermentation) for further neutralisation, which is still only partial. Also, soaking/germination (sprouting) reduces or eliminates phytates.

Still, legumes are an important source of proteins and should be part of a good and varied diet.