Giardia duodenalis infection in humans can cause a variety of clinical symptoms. The relation between clinical symptomatology and the Giardia isolate genotype was studied in 18 Dutch patients infected with G. duodenalis who visited their general practitioner. Contrary to earlier studies, a 100% correlation between severity of diarrhoeal complaints and genotype was found: assemblage A isolates were solely detected in patients with intermittent diarrhoeal complaints, while assemblage B isolates were present in patients with persistent diarrhoeal complaints. These results are significant because they show for the first time that genetically linked features of G. duodenalis are major determinants in the severity of infection in human giardiasis.