Entameba histolytica causes amebiasis, which includes both intestinal and extraintestinal amebiasis. E. histolytica causes 34 million to 50 million symptomatic cases of amebiasis worldwide every year, causing 40 thousand to 100 thousand deaths annually. E. histolytica, the pathogenic species of amebae is indistinguishable in its cyst and trophozoite stages from those of E. moshkovskii, a free-living ameba, and E. dispar, a non-invasive ameba, by microscopy, except in cases of invasive disease, where E. histolytica trophozoite may contain ingested red blood cells, but such a finding is rarely seen. This leads to a confusing scenario for the definite identification and differentiation of E. histolytica from E. moshkovskii and E. dispar by conventional microscopy, in the diagnosis of intestinal amebiasis. The advent of molecular methods such as multiplex PCR and real time PCR have facilitated a better and accurate diagnosis of E. histolytica, E. moshkovskii, and E. dispar in stool, urine, saliva, and other specimens. Multiplex PCR for the diagnosis of amebic liver abscess, using urine and saliva as clinical specimens, has been used, and the results have been encouraging. Real-time PCR is a new and a very attractive methodology for laboratory diagnosis of amebiasis, because of its characteristics that eliminate post-PCR analysis, leading to a shorter turnaround time. Microarray-based approaches represent an attractive diagnostic tool for the detection and identification of amebae in clinical and epidemiological investigations. Development of vaccines against amebiasis is still in its infancy. However, in recent years, progress has been made in the identification of possible vaccine candidates, the route of application, and the understanding of the immune response, which is required for protection against amebiasis. Thus, it is just a matter of time, and hopefully, amebiasis vaccine for human trials will be available in the next few years.