For much of the last hundred years most cases of amoebiasis have been diagnosed by light microscopy. Only relatively recently have we become aware that this technique is usually incapable of distinguishing between two species - Entamoeba histolytica and E. dispar - only the first of which is a pathogen. The implications of this for patient management and, even more, for the validity of epidemiological surveys, are only slowly being addressed. What is clear is that methods are urgently required to distinguish between infections with these two species and this review attempts to summarise some of those, which have been developed to meet this need.