Apart from being highly nutritious and endowed with several health benefits, bamboo shoots contain some anti-nutrients which raise concerns regarding their biosafety. Anti-nutrients are mainly defence-related secondary metabolites produced by plants with specific biological functions. These compounds tend to affect the bioavailability and metabolisms of various essential nutrient components of plants foods if consumed in higher quantities. Anti-nutrients found in bamboo include cyanogenic glycosides, saponins, glucosinolates, tannins, oxalates and phytates, all of which can be removed by processing. The anti-nutrient cyanogenic glycoside is most predominant in bamboo shoots and is known as taxiphyllin which is structurally p-hydroxylated mandelonitrile tiglochinin which is thermolabile and hence can be decomposed readily by the action of heat. Anti-nutrient content in shoots varies from species to species. Species such as Phyllostachys, Melocanna and Chimonobambusa have less cyanogen content and do not require much processing whereas shoots of Bambusa and Dendrocalamus require vigorous processing due to their high cyanogen content. This chapter discusses the anti-nutrients present in young shoots of more than 30 bamboo species, their chemical structures with an explanation of their enzymatic pathways.