In this study we investigated the prevalence of Giardia, and genetic subtypes present in children living in a remote Indigenous community in the Northern Territory. Screening by direct microscopy and 18S rRNA PCR amplification showed that Giardia was highly prevalent in faecal samples collected over an 18 month period. The high prevalence of Giardia detected in this study is similar to high rates of Giardia previously reported for children living in remote Indigenous communities in Australia. The highest prevalence of Giardia was found in 0–,5 year olds, which is similar to that found in low prevalence regions of Australia, where infants aged 0–4 years are the most commonly affected group by sporadic giardiasis. PCR for the 18S rRNA gene proved to be the most sensitive method to detect Giardia in the faecal samples. Of the 58 positive samples, 41.4% of these were detected as positive by microscopy, whilst 93.1% were detected as positive using the 18S rRNA PCR. The sensitivity of PCR detection also differed between the two Giardia loci that were examined. Differences in detection rates for microscopy and PCR screenings are expected due to intermittent and/or low parasite shedding, DNA polymerase inhibitors in faecal material, and differences in gene copy number for the gdh and 18S rRNA loci. Previous studies in remote Indigenous communities of Australia have used microscopy as a preliminary screening tool to determine Giardia positivity, and select samples for downstream molecular analyses. The results of the present study, however, demonstrate that a large proportion of positive cases were only detectable by 18S rRNA PCR. Although detection of Giardia DNA by PCR is not direct evidence of an established infection, PCR is highly sensitive. Similar screening results have been reported from children living in high prevalence regions of Rwanda, and may reflect low parasite shedding due to constant Torin 1 exposure and chronic infections. Giardia was detected in faecal samples from all three collection periods over the 18 month study and high detection rates were maintained over time. A significant increase in PCR positivity, from 45.7% to 70.2%, was detected between collection rounds 1 and 2, and was consistent with an increase in positivity among the 0–,5 year age group over this time. No differences in the frequency of positive cases among males and females, and among assemblage A and B between collection rounds 1 and 2 were detected. Our results suggest an overall increase in PCR positivity during the study; however, further sampling in this community would be required to resolve this. Sample sizes for older age groups were small and participants included in this study were self selected. Participants may have been more likely to provide a faecal sample if gastrointestinal symptoms were present, but additional information pertaining to participant symptoms was not available for this study.