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Using disease notification data, we detected spatio-temporal clusters of cryptosporidiosis and giardiasis across three time periods: (i) 1997\u20132000, (ii) 2001\u20132004, (iii) 2005\u20132008. There was substantial variation in the geographical location and timing of recurrent cryptosporidiosis and giardiasis clusters. Statistically significant (<jats:italic>P<\/jats:italic>\u00a0&lt;\u00a00\u00b705) giardiasis clusters tended to occur in predominantly urban areas with little apparent seasonal influence, while statistically significant cryptosporidiosis clusters were detected in spring, in areas with high livestock land use. The location and timing of cryptosporidiosis clusters suggest an influence of livestock production practices, while urban exposures and host behaviour are likely to influence giardiasis clusters. 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