The objective of this retrospective clinical study was the evaluation of the most important pre-, peri- and post-operative parameters of small animals undergoing intestinal surgery and the assessment of their influence on the clinical outcome. Medical records of dogs (n = 135) and cats (n = 85) undergoing enterotomies or intestinal resection and anastomosis over a period of five years were reviewed. The data were divided into pre-, peri- and post-operative parameters, statistically analysed with regard to the evaluation of risk factors and occurrence of complications and compared between the two species. The overall mortality rate was 20 % with no significant difference between the species. A pre-operative decrease in total protein and hypoalbuminaemia were risk factors. Albumin values below the reference level of 2.6 g/dl were associated with a 3.2-fold increased risk of death. However, peritonitis diagnosed before surgery was not associated with a worse clinical outcome. Intestinal resection and anastomosis, as well as the diagnosis of neoplasia and invagination, were significant predictors of negative outcomes. Furthermore, the need for post-operative intensive care and the need for reoperation due to intestinal dehiscence and peritonitis were associated with a significantly increased risk of death. Low albumin levels, tumours, invagination, intestinal resection and anastomosis, the need for intensive care and peritonitis were associated with a worse prognosis in intestinal surgery in both dogs and cats.