A survey on the presence of Cryptosporidium oocyst and Giardia cyst in livestock drinking water as well as the urban tap water throughout Taiwan was carried out. Water examination for the presence of the protozoa was conducted by filtering through a PTFE membrane followed by immunomagnetic separation (IMS) and immunostaining the sediment with commercially available monoclonal antibody against Cryptosporidium and Giardia. Of the 55 different water samples from various sources examined, 2 were found to contain both of Cryptosporidium oocyst and Giardia cyst, 1 was found to contain Cryptosporidium oocyst only. These protozoa-positive water samples, originating from underground well and from the mountain spring, were also used as drinking water for livestock. However, no Cryptosporidium oocyst was found in the city tap water. This is the first report of Cryptosporidium oocyst and Giardia cyst being found in the drinking water for livestock.