Diarrhoeal diseases in piglets caused by Escherichia coli are responsible for substantial losses each year in the Australian pig industry. A cross-sectional survey was conducted (September 2013-May 2014) across 22 commercial pig herds located in southeastern Australia: NSW (n = 9); VIC (n = 10); and SA (n = 3), to estimate the prevalence of E. coli associated diarrhoea in pre- and post-weaned piglets and to identify key risk factors associated with E. coli disease. A questionnaire on management and husbandry practices was included. Faecal samples (n = 50 from each herd) were tested for the presence of β-haemolytic E. coli. Species level identification was confirmed by matrix-assisted laser desorption / ionisation time-of-flight mass spectrometry (MALDI-TOF/MS). ETEC virulence and enterotoxin genes (F4, F5, F6, F18, F41, STa, STb and LT) were screened for by multiplex PCR. This study assessed 60 potential risk factors for E. coli disease in post-weaned piglets, with 2 key factors-recent disease events and the presence of bedding, statistically associated with the presence of post-weaning scours. The prevalence of diarrhea in pre-weaned pens was 17% (16/93), compared with 24% (24/102) in post-weaned pens. The most prevalent β-haemolytic ETEC genes were F18 (32%) and STb (32%) but isolates were more likely to contain F4:STb (11 of 22 herds, 23%), than F18:STb (5 of 22 herds, 6%). These findings indicate that recent disease events that have occurred within the last 12 months, and by the use of bedding or not maintaining fresh bedding can have significant impacts on piglet diarrhoea.