Abstract Clean Si(001) single crystal surfaces provided different surface reconstructions: p(1 × 2) and c(n × 2) (n = 4, 6) at room temperature. The in situ oxidation of these surfaces was followed by Auger electron spectroscopy and by X‐ray photoelectron spectroscopy. It is found that, in similar ultrahigh vacuum conditions, much faster contamination (about 500 times) occurs when the samples are investigated by AES than by XPS, owing to the interaction of the electron beam with the sample surface. With the sample subject to the AES investigation, the contamination occurs by forming >Si2CO complexes based on the Si dimers. During XPS, reaction with water molecules from the residual gas should also be taken into account.