OBJECTIVE: To describe heart rate variability (HRV) in horses with acute gastrointestinal disease that undergo exploratory laparotomy. We hypothesized that horses with ischemic gastrointestinal disease will have reduced HRV compared to horses with nonischemic lesions. We further hypothesized that a reduction in HRV will be associated with nonsurvival. DESIGN: Prospective, clinical, observational study. SETTING: University veterinary teaching hospital. ANIMALS: Horses presented for acute colic (n = 57) or elective surgical procedures (n = 10) were enrolled. INTERVENTIONS: Admission heart rate (HR) was recorded and within 2 hours of recovery from general anesthesia continuous telemetry was placed, monitored and recorded for 48-52 hours postoperatively. Stored electrocardiograms were manually inspected and R-to-R intervals were extracted and uploaded into HRV software for analysis. Time domain and frequency spectral analysis were investigated at Times 1 (2-10 h), 2 (16-24 h), 3 (30-38 h), and 4 (44-52 h) postoperatively. A two-way ANOVA for repeated measures was used for group comparisons. Logistic regression analysis was used to detect potential associations between admission HR, time and frequency domain variables, and nonsurvival. MEASUREMENTS AND MAIN RESULTS: Horses diagnosed with an ischemic gastrointestinal lesion (n = 22) at the time of surgery had significantly higher postoperative heart rates and reduced time domain-derived measures of HRV than horses with nonischemic gastrointestinal lesions (n = 35) or control horses (n = 10). Horses that survived to discharge had significantly lower postoperative HRs, higher time domain, and lower low frequency spectral measures of HRV compared to nonsurvivors. The multivariable logistic regression model had a receiver operating characteristic area under the curve (AUC) of 0.95 and was significantly better at predicting nonsurvival than admission HR (P = 0.0124). CONCLUSIONS: Reduced HRV was strongly associated with ischemic gastrointestinal disease and nonsurvival. HRV analysis is a noninvasive technique that may provide diagnostic and prognostic information pertinent to the management of postoperative horses with severe gastrointestinal disease.