The National Notifiable Diseases Surveillance System received 8,677 notifications of diseases transmitted by mosquitoes in Australia from 1 July 2008 to 30 June 2009. The alphaviruses, Barmah Forest and Ross River, accounted for 6,574 (78%) of these notifications during 2008-09. There were 1,009 notifications of dengue virus infection locally-acquired in North Queensland and 484 notified cases resulted from overseas travel. Notification rates of dengue virus infection for 2008-09, regardless of where infection was acquired, exceeded the five-year mean rate and may be attributed to increased disease activity in the Asia-Pacific region. North Queensland was the site of several outbreaks of locally-acquired dengue virus infection involving all 4 serotypes. These dengue outbreaks affected several locations with over 1,000 notifications. Detection of flavivirus seroconversions in sentinel chicken flocks across Australia provides an early warning of increased levels of Murray Valley encephalitis virus and Kunjin virus activity. Increased levels of flavivirus activity were detected in western and northern Australia, which prompted public health action. This action preceded 4 notifications of Murray Valley encephalitis infections, 2 (fatal) cases acquired in the Northern Territory and two in Western Australia. There were no notifications of locally-acquired malaria in Australia and 567 notifications of overseas-acquired malaria during 2008-09. This annual report presents information of diseases transmitted by mosquitoes in Australia and notified to the National Notifiable Diseases Surveillance System.