When stunning animals e.g. by CO2-stunning aversive reactions may be seen among the animals as a reaction to the high concentration of CO2. To avoid the aversive reactions animals can be pre-stunned before being final-stunned and perhaps killed or slaughtered when stunned. Pre-stunning of animals may be performed with a combination of gas for pre-stunning comprising at least air and/or O2 together with CO2 e.g. in a concentration below 40%, at least air and/or O2 together with N2O, or at least air and/or O2 together with N2O and CO2, where CO2 may bi in a concentration below 40%. For larger animals such as pigs pre-stunning is performed for less than 60 seconds. A stunning system may comprise means for pre-stunning of animals before performing a final-stunning and may include gas storage for re-use of the pre-stunning gas.