The identification of risk factors for ovine Johne's disease (OJD) prevalence level that producers can influence will improve on-farm control of this disease. A cross-sectional study of 92 infected sheep flocks in Australia was conducted during 2004/2005 to identify such risk factors. Prevalence level based on culture of pooled faecal samples collected from 3-4 year old sheep in each flock was calculated using a method for variable pool size and flocks were classified as low (< 2%), medium (2 to 10%) and high (>10%) prevalence. Information about potential risk factors was gained from interviews with each producer using a questionnaire (OJD flock history, flock management practices and management of the 3-4 year old cohort sheep) and from analysis of soil samples collected from paddocks grazed by the cohort sheep as lambs, weaners and hoggets or adults (pH, texture and fertility). Univariable and multivariable analyses were conducted to identify risk factors statistically associated with OJD prevalence, and to quantify the magnitude and direction of identified relationships after allowing for potential confounding factors, including time since infection, livestock purchases, vaccination and culling practices. The implications for understanding the epidemiology of OJD and on-farm disease control will be discussed.