A survey on benzimidazole (BZ) resistance in small strongyles was performed on three farms in the tenth region in Chile. Samples from a total of 100 horses were tested using the faecal egg count reduction test (FECRT), the egg hatch assay (EHA) and an allele-specific PCR for the detection of beta-tubulin isotype 1 genes coding for phenylalanine (phe) or tyrosine (tyr) at codon 200. In the past, BZ-type drugs have been used within anthelmintic campaigns on all the three farms. This has predictably led to a high degree of BZ resistance at the Valdivia and Riñihue farms and to a lesser degree at the Frutillar farm, as demonstrated by all the three tests. The FECRT indicated resistance in every farm by faecal egg count reductions (FECR) of 27% (S.D. +/- 33), 26.5% (S.D. +/- 26.9) and 83.9% (S.D. +/- 22.8) for the Valdivia, Riñihue and Frutillar farms, respectively. With the EHA, the following mean LD(50) values were found before and after treatment with fenbendazole (FBZ): 0.093, 0.141 and 0.066 microg TBZ/ml and 0.149, 0.158 and 0.091 microg TBZ/ml, respectively, for the Valdivia, Riñihue and Frutillar samples. The corresponding LD(96) values were 0.222, 0.263 and 0.188 microg TBZ/ml before treatment and 0.316, 0.322 and 0.221 microg TBZ/ml after treatment, indicating BZ resistance in all the cases. Genotyping was performed on more than 1700 single larvae, at least 10 per faecal sample, for 98 pre- and 66 post-treatment samples. Despite a general trend toward higher percentages of phe/tyr and tyr/tyr individuals following treatment, no statistically significant difference was found between these two and the phe/phe genotype percentages. However, a significantly negative correlation was detected between the LD(50) values and the phe/phe percentages and there was a positive correlation between the FECRT results and the phe/phe percentages. Thus, there seems to be a difference in the significance of the codon 200 polymorphism in the mechanisms of BZ resistance in small strongyles of the horse and sheep trichostrongyles.