Cystic echinococcosis (CE) is a zoonotic helminthic disease, which is widely distributed throughout the world. Although G1 is the Echinococcus granulosus genotype most commonly involved in CE in humans, the prevalence of infection with other genotypes, such as G6, may be higher than previously thought. We performed molecular analysis to identify which E. granulosus genotypes are the causative agents of CE in humans in Kenya's Turkana district. During a Hydatid Control Programme in 1993-1994, 71 cyst fluid isolates of E. granulosus were collected during PAIR (puncture, aspiration, injection, re-aspiration) sessions. DNA was amplified for two genes from 59 isolates. Of these, 49 isolates (83%) were identified as G1 and 10 (17%) as G6. This is the highest prevalence of G6 detected in humans of the Old World, and our results suggest that, in highly contaminated environments, G6 might be of greater public health significance than previously believed.