We investigated if long-lasting (5 h) anaesthesia with isoflurane has different pharmacological effects in two different rat strains: Wistar and Sprague Dawley. The mean blood pressure was 34% higher in Sprague Dawley rats as compared to the Wistar rats (p = 0.04). In Wistar rats, the pH value decreased to 7.1, lactate increased by 53%, creatinine increased 2.7-fold, alanine amino transferase and aspartate amino transferase increased more than 4-fold and lactate dehydrogenase increased 9-fold (p < 0.05). There were no changes in laboratory parameters in Sprague Dawley rats. This indicates that the Wistar rats were more sensitive to a 5 h anaesthesia with isoflurane after a premedication with ketamin/xylazine in the described study design.