The Planetary Fourier Spectrometer (PFS) onboard the Mars Express (MEX) Mission is a double pendulum interferometer working in two wavelength ranges (1.2 to 5.9 μm and 5.9 to 40 μm). These channels are indeed detected by two separate instruments one on top of the other, with different optical axis alignments. Analysis of in-flight measurements of Mars and Phobos indicates that pre-launch optical alignment measurements do not describe the in-flight pointing characteristics of the two PFS channels. Pre-launch pointing characterization measurements were made with the PFS alone prior to spacecraft integration. It is suspected that disturbances experienced by the PFS during spacecraft integration and especially during launch may have affected its optical alignment. Daily observations of the planet, its limb, and Phobos have been used to retrieve the real pointing directions for the two PFS channels, by applying a method based on the division of the field-of-view cone in 24 angular sectors.