Subcloned lines of the WB strain of Giardia lamblia contain polymorphic ribosomal RNA (rRNA) encoding chromosomes (Le Blancq et al., Nucl. Acids Res. 1991, 19, 4405-4412). We show that in a continuously propagated culture of G.lamblia trophozoites the proportion of trophozoites with rearranged rRNA encoding chromosomes gradually increases, consistent with the high mutation rate of about 1% per cell per division cycle. This conclusion is based on the finding in one experiment that after about 8 division cycles 20% of the population consisted of independent mutants, while after approximately 100 division cycles 87.5% of the population were independent mutants. In a second experiment, approximately 38% and 71.5% of the trophozoites were independent mutants after approximately 9 and approximately 100 division cycles, respectively. The data show that the genome of the WB strain of G.lamblia has a highly recombinogenic phenotype. Extensive karyotype heterogeneity has also been observed among recently isolated G.lamblia strains obtained from a defined geographic area (Korman et al., J. Clin. Invest. 1992, 89, 1725-1733) suggesting that a high mutation rate might also occur in vivo.