Laminitis in the horse is associated with the over consumption of rapidly fermentable carbohydrate, in the form of simple sugars, fructans and/or starch. The fermentation of excessive carbohydrate in the hind-gut can result in the production of lactic acid and other toxins which in turn may act as “laminitis trigger factors.” (Crawford et al., 2007). However, whilst it is known that susceptibility to laminitis varies within the equine population, little is known about the factors governing this variation. We have previously shown that 16S rRNA t-RFLP profile from bacteria extracted from equine faeces clustered weakly into two clades representing normal versus laminitis-prone ponies suggesting a difference in gut microflora between the two groups (Newbold et al., 2008). Here we have extended this observation using real time PCR to investigate changes in the number of streptococci and lactobacilli in the faeces of normal and laminitis-prone ponies following fructan administration.