Abstract 
Background: Acquired Equine Polyneuropathy in Nordic horses (AEP) is the most prevalent equine polyneuropathy in Norway, Sweden and Finland. AEP is characterized by pelvic limb knuckling due to metatarsophalangeal extension dysfunction. 
Objectives: To evaluate function of descending motor pathways in AEP using transcranial magnetic stimulation (TMS).  
Study design: An analytical, observational cohort design 
Methods: Clinical findings and TMS results of 20 horses from an AEP outbreak in Sweden were evaluated at two timepoints with 5 months interval. Latency time (LT) in milliseconds (ms) between coil discharge and onset of muscle potential was recorded for thoracic and pelvic limbs.
Results: Fourteen affected horses showed knuckling, and 6 horses were neurologically sound at first visit. Thirteen affected horses had improved clinically five months later, four no longer showed knuckling. Motor neurological dysfunction with increased LT was confirmed by TMS in all 14 affected horses at both visits. Mean difference in LT from normalized reference values (ΔLT) in pelvic limbs of affected horses was +12.95 ms (+38%) at first examination (1.9-29.6 ms; SD 1.23; n=14), and +8.1 ms (+24%) five months later (1.0-18.9 ms; SD 1.21; n=14), cutoff >0.8 ms. Eleven of 14 affected horses also presented delayed TMS responses in thoracic limbs, with up to 14% ΔLT increase. Neurologically sound, non-lame horses (n=8) showed mean ΔLT -0.5 ms ( -1.8 to 0.2 ms; SD=0.64) in pelvic, and -0.35 ms (range, -0.7 to 0 ms; SD=0.26; n=8) in thoracic limbs, cutoff >0.2 ms.  
Limitations: Examinations were only repeated once for organizational reasons.
Conclusion: This study proved involvement of motor pathways in AEP. Findings add to previously established involvement of sensory nerve fibers. Sensory and motor involvement contribute to mismatch of ascending and descending nerve signals, which contributes to the clinical manifestations. 
TMS may be useful in evaluating clinical and subclinical cases of AEP.