Equine transportation is associated with a variety of serious health disorders causing economic losses. However; statistics on horse transport are limited and epidemiological data on transport related diseases are available only for horses transported to abattoirs for slaughter. This study analysed reports of transport related health problems identified by drivers and horse owners for 180 journeys of an Australian horse transport company transporting horses between Perth and Sydney (~4000 km) in 2013'2015. Records showed that 97.2% (1604/1650) of the horses arrived at their destination with no clinical signs of disease or injury. Based on the veterinary reports of the affected horses; the most common issues were respiratory problems (27%); gastrointestinal problems (27%); pyrexia (19%); traumatic injuries (15%); and death (12%). Journey duration and season had a significant effect on the distribution of transport related issues (p < 0.05); with a marked increase of the proportion of the most severe problems (i.e., gastrointestinal; respiratory problems and death) in spring and after 20 h in transit. Although not statistically significant; elevated disease rate predictions were seen for stallions/colts; horses aged over 10 years; and Thoroughbreds. Overall; the data demonstrate that long haul transportation is a risk for horse health and welfare and requires appropriate management to minimize transport stress.