A flow cytometry (fluorescence-activated cell sorter)-based assay was adapted to detect and quantify antibodies to Balamuthia mandrillaris, a causative agent of fatal amoebic encephalitis (BAE), and to Acanthamoeba species. With sera from BAE patients for positive and a group of inconspicuous volunteers for negative reference, most of the 237 sera from random blood donors, patients with atypical encephalitis, atypical pneumonitis, visceral amoebiasis and toxoplasmosis and from subjects working with primates and other mammals were rated negative, 19% elevated and of these 2% high. In comparison, 23 of 25 West Africans living in rural areas revealed elevated, of these 15 high, and one very high B. mandrillaris-binding antibody titers, the latter well in the range of BAE patients. To date, none of the tested individuals have developed symptoms indicative of BAE. Criss-cross analysis with rabbit hyper immune sera against B. mandrillaris, Acanthamoeba comandoni (group 1), Acanthamoeba castellanii (group 2) and Acanthamoeba lenticulata (group 3) confirmed that cross-reactivity between B. mandrillaris and Acanthamoeba sp. is negligible while accentuating antigenic differences between the three morphological groups of Acanthamoeba.