The faecal worm egg count (FWEC) procedure is the most widely used method of quantifying the nematode burden of horses, and is frequently used in clinical practice to inform treatment and prevention practices. Despite the importance of the test and the known variability in FWEC taken from a single animal, the underlying source of this variability has not been quantified. Here, we present a statistically robust method of partitioning the variability in observed FWEC from domestic animals, and intensively sampled data are used to quantify the relative importance of multiple potential sources of variability in horses infected with cyathostomins. The results demonstrate that a substantial proportion of the observed variability in FWEC between samples occurs as a result of variability within an animal, with the major sources of this variability being due to local aggregation of eggs within faeces and variation in egg concentration between faecal piles. The McMasters procedure itself is associated with a comparatively small source of variability, and is therefore highly repeatable when a large enough number of eggs is observed to minimise the error associated with the counting process. We conclude that the variation between samples taken from the same animal is likely to be substantial, and should either be explicitly included or controlled for in future longitudinal equine FWEC studies. The use of larger homogenised faecal samples to improve the repeatability of FWEC from an individual animal is also recommended.