Size variations in homologous chromosomes from six Giardia lamblia isolates have been demonstrated. Four or five intensely stained (major) bands as well as a variable number of lightly stained (minor) bands are present in pulsed field gradient separations. Southern blot analysis with total chromosomal DNA as well as chromosome specific probes indicates that each minor band cross-hybridizes with a major band. Minor bands of doubly cloned organisms appear identical to those of parent clones, indicating that the minor bands do not reflect the presence of variant members within the total population of trophozoites. Densitometric comparisons of chromosome bands from known numbers of Plasmodium falciparum ring stage forms and known numbers of Giardia trophozoites suggest that minor bands MBa and MBb are present in each Giardia trophozoite. Comparison of Not I restriction fragments from the major and minor bands reveals common restriction fragments. Taken together, the data imply that sets of closely related chromosomes occur in the Giardia trophozoite.