Introduction: Clinical doses of anaesthetic agents were administered to rabbits and effects on the brain, heart, and liver were investigated biochemically and histopathologically. Material and Methods: The rabbits were randomly divided into three main groups (16 rabbits each) and each group into study (n = 8) and control (n = 8) groups. All study group rabbits received 3 mg/kg of midazolam (M) intramuscularly. Group 1.1 (M) received nothing further, group 2.1 (MK) also received 25 mg/kg of ketamine, and group 3.1 (MKI) besides ketamine was also given 2% isoflurane to induce anaesthesia for 30 min. NaCl solution in the same volume as midazolam and ketamine was injected into the controls. Results: In clinical evaluation significant differences were detected in respiratory and heart rates. In blood gas analysis the PO2 and PCO2 values showed statistical differences in anaesthesia intervals. Significant biochemical value changes were recorded in creatine kinase-Mb, glucose, and total protein. Histopathological liver examinations revealed higher total apoptotic and normal cell numbers in the MK than in the M and MKI groups. Apoptotic cell numbers were statistically significant in M and MK groups. Conclusion: Anaesthetic agents may increase programmed apoptosis. The MKI anaesthetics combination was found to cause less cell destruction in general than the other study groups. It was indicated that MKI was the safer anaesthetic combination in rabbits.