An online survey was conducted to determine associations between transport management and transport-related injuries and diseases in horses in Australia. The survey was composed of three sections: respondents' demographic information, transport management strategies or procedures (before, during and after transportation) and transport diseases experienced in the previous two year period. Univariate and multivariate modelling was performed exploring associations between variables (respondents' details and transport management strategies) and the following transport-related diseases as outcomes: traumatic injuries, diarrhoea, heat stroke, muscular problems, laminitis, transport pneumonia and colic. The survey generated 797 responses. Traumatic injuries were the most common transport-related problem, with a reported incidence of 45.0%. Younger respondents (<40 years old) caring for large numbers of horses (>30 in a week) were more likely to report transport-related injuries. Injury risk was also linked to the use of protections and tranquilizers prior to transport, and checking horses after the journey. Diarrhoea (20.0%) and heat stroke (10.5%) were reported more by amateur than professional horse carers. Increased risk of heat stroke was linked to the restriction of hay and water prior to transportation. Muscular problems (13.0%) appeared to be exacerbated when horse health was not assessed before journey; whilst the risk of laminitis (2.9%) was around three fold greater when post transport recovery strategies were not applied. Associations were made between transport pneumonia (9.2%) and duration of journey, and with activity (horses involved in racing at greater risk). No associations were seen between the incidence of colic (10.3%) and the variables examined. Study findings should be interpreted with caution as they represent participant perceptions and recall. Nevertheless, results support many current recommendations for safe transportation of horses. They also highlight the need to further investigate many of identified management factors to refine existing policies and practices in equine transportation.