The efficacy of phenotypic assessments to detect anthelmintic resistance can fluctuate substantially. In some cases, the level of anthelmintic resistance may be overestimated. The main factors associated with “false resistance” include: the use of low quality drugs (some generic drugs), poor absorption or metabolisation of the drug, or, under dosing. Conversely, anthelmintic resistance may be underestimated due to lack of reliable indicators and surveys. Anthelmintic resistance has been almost entirely studied in gastro-intestinal nematodes (GIN), although resistance has also been demonstrated or suspected in liver fluke and the cestode Moniezia. Determining anthelmintic resistance in GIN field studies is based exclusively on phenotypic evaluation, the evolution of faecal egg counts before and after a treatment, and in a few instances, on actual worm counts. Several important points need to be considered in determining the reliability of GIN faecal egg counts such as: i) the sampling procedure of faeces (individual or composite), ii) the sampled animals (high versus low infection level, number of samples) iii) the moment of sampling after treatment (long enough to detect a decrease in egg counts but not too long so reinfection could then interfere with results), and iv) the mode of calculation (basedon individual or average efficacy, each of which has several potential methods of calculation). In this chapter, we evaluate the relative importance of each of these four points. To do this, we gather results from various studies obtained from the literature and from as yet unpublished original research from our own datasets and from those provided by other researchers. We conclude by discussing the potential of using faecal egg counts as an indicator to evaluate anthelmintic resistance, and its place in GIN management.