A review was conducted to examine published works that focus on the complex epidemiology ofEnterocytozoon bieneusiinfection in humans. Studies on the prevalence of these emerging microsporidian pathogens in humans, in developed and developing countries, the different clinical spectra ofE. bieneusiintestinal infection in children, in different settings, and the risk factors associated withE. bieneusiinfection have been reviewed. This paper also analyses the impact of the recent application of PCR-based molecular methods for species-specific identification and genotype differentiation has had in increasing the knowledge of the molecular epidemiology ofE. bieneusiin humans. The advances in the epidemiology ofE. bieneusi, in the last two decades, emphasize the importance of epidemiological control and prevention ofE. bieneusiinfections, from both the veterinary and human medical perspectives.