The prevalence and nature of arrhythmias in horses following general anaesthesia and surgery is poorly documented. It has been proposed that horses undergoing emergency surgery for gastrointestinal disorders may be at particular risk of developing arrhythmias. Our primary objective was to determine the prevalence and nature of arrhythmias in horses following anaesthesia in a clinical setting and to establish if there was a difference in the prevalence of arrhythmias between horses with and without gastrointestinal disease undergoing surgery. Our secondary objective was to assess selected available risk factors for association with the development of arrhythmias following anaesthesia and surgery. Horses with evidence of gastrointestinal disease undergoing an exploratory laparotomy and horses with no evidence of gastrointestinal disease undergoing orthopaedic surgery between September 2009 and January 2011 were recruited prospectively. A telemetric electrocardiogram (ECG) was fitted to each horse following recovery from anaesthesia and left in place for 24 hours. Selected electrolytes were measured before, during and after surgery and data was extracted from clinical records for analysis. Recorded ECGs were analysed and the arrhythmias characterised. Multivariable logistic regression was used to identify risk factors associated with the development of arrhythmias. Sixty-seven horses with gastrointestinal disease and 37 without gastrointestinal disease were recruited. Arrhythmias were very common during the post-operative period in both groups of horses. Supra-ventricular and bradyarrhythmias predominated in both groups. There were no significant differences in prevalence of any type of arrhythmias between the horses with or without gastrointestinal disease. Post-operative tachycardia and sodium derangements were associated with the development of any type of arrhythmia. This is the first study to report the prevalence of arrhythmias in horses during the post-operative period in a clinical setting. This study shows that arrhythmias are very common in horses following surgery. It showed no differences between those horses with or without gastrointestinal disease. Arrhythmias occurring in horses during the post-anaesthetic period require further investigation.