Giardia intestinalis has been reported in newborn calves world-wide; however, information on the extent of G. intestinalis in New Zealand calves has to date been very limited. The current study attempted to establish the prevalence rate of G. intestinalis in calves up to 8 weeks old in New Zealand. More than 700 calf fecal specimens were collected during the spring calving seasons of 1998 and 1999 from two regions in North Island, New Zealand (Manawatu and Waikato) and tested for the presence of G. intestinalis. In addition to determining the presence of G. intestinalis in newborn calves, sequence analysis was performed using specific amplification primers developed to target a section of the ribosomal DNA (rDNA). This locus is considered to be rapidly evolving, and therefore, suitable for use in the elucidation of phylogenetic relationships between G. intestinalis isolates. Sequencing was performed using G. intestinalis DNA extracted from cysts collected directly from the calf fecal matter. There was no culturing of the G. intestinalis isolates either in vivo or in vitro. Over 40% of all collected calf fecal specimens contained G. intestinalis cysts and rDNA sequence analysis revealed two different sequences among calf isolates. These sequence differences were not found to correspond to a particular season, geographical region or farming practice. Preliminary phylogenetic analysis suggests that these two rDNA sequence types are indicative of calf hosts.