To investigate drug sensitivities of human Giardia isolates, we developed a reproducible in vitro 3H-thymidine uptake assay to compare drug potencies. Among 13 Giardia intestinalis stocks obtained from the culture of trophozoites isolated from duodenal juice, considerable variation in susceptibility to a range of currently used drugs was found. The population doubling time of these stocks also varied widely. Clinical features in patients ranged in severity from mild chronic diarrhea to a celiac-like syndrome, with a similar variation in the degree of histologic change in the mucosa. Brush-border enzyme activities were universally reduced in children younger than 5 years of age. The two isolates with the highest ID50 values for furazolidone in vitro were from patients who had persistent symptoms after treatment with this drug; these patients subsequently responded to treatment with a nitroimidazole with greater in vitro potency. These studies suggest that biologic variants of G. intestinalis exist in humans and may in part account for the variable clinical manifestations and for some treatment failures.