Background With intensive use of anthelmintic drugs in recent decades, anthelmintic resistance (AR) in horse nematodes is becoming a growing issue in many countries. However, there is little available information about the parasites, treatment practices or AR in the horse population in Lithuania. The aim of this study was to assess the current situation of AR on horse farms in Lithuania. The study was conducted in 25 stables on horses with a strongyle faecal egg count (FEC) of >= 200 eggs per gram. A faecal egg count reduction test (FECRT) was performed on each farm after administration of ivermectin (IVM) or pyrantel (PYR). Results The efficacy of IVM was comparatively high, with 98.8% of 250 horses having a zero egg count 14 days after treatment. Two conditions were used to interpret the FECRT results for PYR: firstly, resistance was determined when FECR was < 90% and the lower 95% confidence interval (LCL) was < 80%, and secondly when in addition the upper confidence level (UCL) was < 95%. Under the first condition, resistance against PYR was found in five stables (25% of all tested herds), while when considering the UCL as well, resistance was only detected in two stables (8%). The FEC showed a significant (P < 0.01) difference between the treatment and control groups. Only cyathostomin larvae were detected in larval cultures derived from strongyle-positive faecal samples collected 14 days after treatment of a test group with PYR. Conclusions This in vivo study showed that PYR resistance is prevalent on horse farms in Lithuania, while the efficacy of IVM still appears to be unaffected. However, further studies of ivermectin resistance are needed. These findings should guide the implementation of more sustainable management of strongyle infections in horses in Lithuania.