Giardia and Cryptosporidium have emerged as waterborne pathogens of concern. Twenty-six water samples were collected from small water systems in Taiwan and checked for the occurrence of both parasites. Water quality parameters and characteristics of the sampling sites were also recorded. The frequencies of occurrence for Giardia and Cryptosporidium were 46.2% for each; and their mean concentrations were 79.5 cysts/100 1 and 22.1 oocysts/100 1, respectively. The concentrations of oocysts and heterotrophic bacteria exhibited the highest correlation and followed the concentrations of the two protozoa. The water samples from sites with filtration devices had a lower oocyst concentration than those from sites without filtration devices, while no significant difference was found for cysts. The level of each parasite had no direct relationship with altitude. The cyst concentrations increased proportionally with the consumer population using the water systems. Risk assessment of the parasitic infections suggests that setting up disinfection devices in the small water systems would be needed.