Diarrhoeal disease (scours) in piglets, often associated with enterotoxigenic Escherichia coli (ETEC), is a substantial financial burden to the pig industry worldwide. Previous research has not explicitly examined the relationships between farm, pen and microbiological factors. Here we present a state of the art analysis to reveal empirical indirect - as well as direct - associations between management factors as putative risks for scours in pre- and post-weaned piglets. A Bayesian Network is constructed to identify the optimal structural model describing the relationships between risk factors. An additive model is then built to estimate more epidemiologically familiar odds ratios. Farm-level variance dominates the model, making many pen-level associations null. However, there is evidence that pre-weaning scours are less likely on farms with <400 sows (0.14, 0.03-0.50). Our results strongly suggest that smaller production units (piglets/pen) could reduce the incidence of scours in piglets. There is also some evidence that ownership of other livestock is a potential risk factor for pre-weaning scours, although this was observed only at one farm. Future research should be directed at better understanding the role of herd size and investigating the relationship between managing other livestock and the occurrence of scours in pig herds.