There have been 5 confirmed cases of Murray Valley encephalitis virus (MVE) infection in the Alice Springs region during the high rainfall years of 1999/00 and 2000/01, compared with one case in the preceding 9 years. There also appeared to be an increased prevalence of Ross River virus (RR) infection in the Alice Springs and Tennant Creek regions associated with high rainfall. This paper presents an analysis of summer rainfall from 1990/91 to 2000/01, numbers of seroconversion of sentinel chickens to MVE, and RR cases in both regions. In Alice Springs where summer rainfall (December to February) and average vector numbers in the December to March period are closely correlated, the analysis also included mosquito vector numbers and MVE cases. Summer rainfall over 100 mm was significantly associated with sentinel chicken seroconversions to MVE. From December to March there was also a significant association of average vector numbers (> or = 300) with seroconversions in sentinel chickens following high summer rainfall. MVE appears enzootic in the Tennant Creek region and epizootic in the Alice Springs region. In Alice Springs during December to March, there was a significant association of RR cases with rainfall over 100 mm and with average vector numbers over 300. There was also a significant correlation of summer rainfall with RR cases in Tennant Creek. Summer rainfall is a new and good early indicator of high risk for both MVE and RR disease in the Alice Springs locality and RR in the Tennant Creek locality. Although similar relationships between rainfall and vector abundance, and disease incidence probably exist in other areas of central Australia, rainfall and vector abundance thresholds will probably vary according to local climatic and environmental conditions.