Carbon dioxide (CO2) is one of the most commonly used euthanasia agents for mice, yet it is highly aversive and nociceptive. Inert gases are a possible alternative, however there are qualitative reports of seizures resulting from exposure. Here we evaluate epileptiform activity caused by inert gases (N2, He, Ar and Xe) and CO2 in mice chronically instrumented for EEG/EMG undergoing single-gas euthanasia. We found that N2, He and Ar caused epileptiform activity in all animals, CO2 in half of animals and no epileptiform activity produced by Xe. Atmospheric O2 concentrations at epileptiform activity onset were significantly higher for CO2 than for all other gases and occurred soon after loss of motion, whereas N2 and Ar epileptiform activity occurred at cessation of neocortical activity. Helium caused the longest epileptiform activity and these commenced significantly before isoelectric EEG. We did not detect any epileptiform activity during active behaviour. Taken together, these results demonstrate that whilst epileptiform activity from inert gases and particularly Ar and N2 are more prevalent than for CO2, their occurrence at the onset of an isoelectric EEG is unlikely to impact on the welfare of the animal. Epileptiform activity from these gases should not preclude them from further investigation as euthanasia agents. The genesis of epileptiform activity from CO2 is unlikely to result from hypoxia as with the inert gases. Helium caused epileptiform activity before cessation of neocortical activity and for a longer duration and is therefore less suitable as an alternative to CO2.