Clonally derived trophozoites (clone O2-4A1, from a sheep) of the morphologically defined group of Giardia duodenalis change their cysteine-rich surface proteins (CRISPs) spontaneously during in vitro culture. This phenomenon constitutes a serious obstacle for studies that rely on a pure population of cells bearing a particular variant CRISP. We describe herein the successful separation and quantitation of a trophozoite subpopulation expressing a 90-kDa major surface antigen (CRISP-90) from a heterologous population using fluorescence-activated cell sorting (FACS) on the basis of fluorescein-tagged antibodies directed specifically against O2-4A1 CRISP-90. During subsequent in vitro culture, the purified cell population exhibited a progressive decline in the proportion of cells labeled by CRISP-90 specific antibodies. After 46 generations, only one-third of the total trophozoite population reacted with the anti-CRISP-90 antibodies.