The present study aims to investigate whether the disease complex for Haemorrhagic Enteritis (HE) in goats during the winter months is the same as described for Jejunal Haemorrhage Syndrome (JHS) in cattle. The further goal is to determine whether prebiotic and probiotic management strategies developed for JHS in cattle alleviate HE in goats. The clinical, necropsy and microbiologic findings were evaluated for goat cases during a natural HE outbreak. Bacterial pathogens were identified using selective media, biochemical tests, latex agglutination tests and DNA microarray. Feed components were evaluated for mycotoxigenic fungi and mycotoxins. Common clinical signs included stary look, grinding of teeth, an odd twisting of the neck when standing, hind-limb paralysis, rumen stasis, no faecal pellets, profuse drooling and a 50% drop in milk production. A prebiotic/probiotic treatment resolved the symptoms in 14 of 28 goats, but new cases continued to develop. The most common morphologic diagnosis at necropsy was severe jejunitis with intraluminal haemorrhage or blood clots confirming HE. The corn silage contained mycotoxigenic fungi and mycotoxins. There were mixtures of Shiga toxin -producing Escherichia coli (STEC) isolated from the jejunum. The probiotic and prebiotic acted as anti-adhesive agents for STEC colonization in vitro. The prebiotic also acted as a mycotoxin binder in vitro. Removing the mouldy corn silage stopped the mycotoxicosis, but did not correct production losses. Adding a prebiotic or probiotic significantly increased milk production and body condition, but also decreased somatic cell counts. Results confirm that the disease complex for HE in dairy goats consuming mouldy feeds includes mycotoxins and STEC infection. The study also supports the use of prebiotics and probiotics to alleviate the morbidity and production losses associated with the mycotoxicosis.