Structure characterization and biological evaluation of the compounds isolated from Helianthemum glomeratum, particularly that of the polyphenols, has been the aim of a series of studies carried out to define the further potential use of this plant in the treatment of infectious diarrhoea in children. The flavan-3-ols, (-)-epigallocatechin and (-)-epigallocatechin gallate, isolated from Helianthemum glomeratum roots were tested for their antiamoebic and antigiardial effects in vitro. Compared with the activity determined with the leaf and the root methanol extracts, the effect of (-)-epigallocatechin against Entamoeba histolytica was of a similar potency, nevertheless, it also suppressed the growth of Giardia lamblia in axenic cultures, a parasite that proved to be resistant to the crude extracts. It might be assumed that determined biological properties are due to the presence of (-)-epigallocatechin in the plant, although the flavonoids, kaempferol and tiliroside isolated from the leaves, could account for the antiprotozoal properties of this herbal resource, used in Mayan traditional medicine for the treatment of bloody diarrhoea.