Abstract: Background- Horses with endotoxemia often have persistent tachycardia +/- arrhythmias. Heart rate variability (HRV) decreases in other species following endotoxin administration but has not been documented in horses. Objectives- Quantify the changes in HRV following low-dose endotoxin administration. Animals- Thirteen adult, systemically healthy horses were enrolled with normal physical examination, hematology, biochemistry, cardiac troponin, echocardiography, and ECG.Methods- Horses were administered E. coli LPS 30 ng/kg IV. Echocardiography and 24-hour Holter ECG were performed. Treatment with intravenous fluids, polymyxin B and flunixin meglumine was administered at 5hrs. Frequency and type of arrhythmias were documented. Time, frequency and nonlinear domain HRV analysis were performed before, during and after endotoxin administration. Results- Before treatment (time 0-5 hours) 11/13 horses had atrial premature complexes, 6/13 had ventricular premature complexes and 7/13 had sinus block or sinus arrest. Compared to the entire Holter, during the first hour following endotoxin administration the Parasympathetic Nervous System Index decreased and the Sympathetic Nervous System (SNS) Index increased (mean difference: 1.44 and -1.22 respectively, P<0.0001 and P<0.0001) indicating SNS stimulation. Indices of overall HRV showed significant differences, the Standard Deviation of Normal-Normal intervals was decreased at 3-5 hour (Mean difference: 65, P=0.0239) and the Triangular index of NN intervals was significantly decreased at 0-1, 1-3 and 3-5 hour (Mean difference: 1201, 1019, 1284, P=0.0032, 0.0145 and 0.0017 respectively). Indices of short-term variability were not different. Conclusions and clinical importance- Low-dose endotoxin administration causes arrhythmias and SNS stimulation. Analysis of HRV could be considered in monitoring cases of clinical endotoxemia.