In the history of Mars exploration its atmosphere and planetary climatology aroused particular interest. In the study of the minor gases abundance in the Martian atmosphere, water vapour became especially important, both because it is the most variable trace gas, and because it is involved in several processes characterizing the planetary atmosphere. The water vapour photolysis regulates the Martian atmosphere photochemistry, and so it is strictly related to carbon monoxide. The CO study is very important for the so-called “atmosphere stability problem”, solved by the theoretical modelling involving photochemical reactions in which the H 2O and the CO gases are main characters. The Planetary Fourier Spectrometer (PFS) on board the ESA Mars Express (MEX) mission can probe the Mars atmosphere in the infrared spectral range between 200 and 2000 cm −1 (5–50 μm) with the Long Wavelength Channel (LWC) and between 1700 and 8000 cm −1 (1.2–5.8 μm) with the Short Wavelength Channel (SWC). Although there are several H 2O and CO absorption bands in the spectral range covered by PFS, we used the 3845 cm −1 (2.6 μm) and the 4235 cm −1 (2.36 μm) bands for the analysis of water vapour and carbon monoxide, respectively, because these ranges are less affected by instrumental problems than the other ones. The gaseous concentrations are retrieved by using an algorithm developed for this purpose. The PFS/SW dataset used in this work covers more than two and a half Martian years from Ls=62° of MY 27 (orbit 634) to Ls=203° of MY 29 (orbit 6537). We measured a mean column density of water vapour of about 9.6 pr. μm and a mean mixing ratio of carbon monoxide of about 990 ppm, but with strong seasonal variations at high latitudes. The seasonal water vapour map reproduces very well the known seasonal water cycle. In the northern summer, water vapour and CO show a good anticorrelation most of the time. This behaviour is due to the carbon dioxide and water sublimation from the north polar ice cap, which dilutes non-condensable species including carbon monoxide. An analogous process takes place during the winter polar cap, but in this case the condensation of carbon dioxide and water vapour causes an increase of the concentration of non-condensable species. Finally, the results show the seasonal variation of the carbon monoxide mixing ratio with the surface pressure.