CO2 measurements on the EPICA (European Project for Ice Coring in Antarctica) DML ice core in depth levels just below the bubble ice–clathrate ice transformation zone (1230–2240 m depth) were performed. In the youngest part (1230–1600 m), they reveal variations of up to 25 ppmv around the mean atmospheric concentration within centimetres, corresponding to a snow deposition interval of a few years. Similar results are found at corresponding depth regions of the Dome C and the Talos Dome ice cores. Since we can exclude all hitherto known processes altering the concentration of CO2 in ice cores, we present a hypothesis about spatial fractionation of air components related to episodically increasing clathrate formation followed by diffusion processes from bubbles to clathrates. This hypothesis is supported by optical line-scan observations and by O2/N2 measurements at the same depth where strong CO2 variations are detected. Below the clathrate formation zone, this small-scale fractionation process is slowly smoothed out, most likely by diffusion, regaining the initial mean atmospheric concentration. Although this process compromises the representativeness of a single CO2 measurement on small ice samples in the clathrate formation zone of an ice core, it does not affect the mean atmospheric CO2 concentration if CO2 values are averaged over a sufficiently long depth scale (> 10 cm in case of the EPICA DML ice core).