Hendra virus (HeV) produces high mortality rates amongst both horses, and subsequently in-contact humans, when it spills over from its natural host (flying-foxes, genus Pteropus). Over a period of twenty years (1994-2014) there have been 52 recorded HeV incidents, with a total of 90 horses and 7 humans infected; 4 fatally. The Australian winter of 2011 saw an “unprecedented” number of HeV incidents with 18 occurring in the states of Queensland and New South Wales. This represented a major departure from the annual number and distribution of HeV incidents previously seen. The years 2012 and 2013 continued to see relatively high numbers of HeV incidents. In order to explain the high number of HeV incidents in recent consecutive years we undertook a unique retrospective analysis of 2,552 horses submitted for HeV testing at Queensland’s state veterinary reference laboratory, Biosecurity Sciences Laboratory (BSL, Biosecurity Queensland, Department of Agriculture and Fisheries) between 1994-2014. We examine case characteristics provided to the laboratory, such as age, breed, clinical signs (neurological and respiratory), location (north or south of the Tropic of Capricorn), season, sex, year and look for trends in submission rates or risk factors for infection in horses. The adjusted mean prevalence of HeV in horses submitted to BSL was 2.1%. The number of horses submitted for HeV testing increased dramatically after the availability of a local diagnostic PCR (2008, from 1/2 months to 9/week) and after the first detection of HeV in each calendar year from 2008-2011 (from 3 to 22/week, P<0.01) but not for 2012-2014, where the submission rate remained steady (9/week, P=0.10). Significant variables identified in the generalised linear model included breed, clinical signs, location, the interaction between location and year, and season. This is the first comprehensive study to examine risk factors for HeV infection in horses.