We present a study on the properties of electromagnetic plasma waves in the region upstream of the Martian bow shock, detected by the magnetometer and electron reflectometer (MAG / ER) onboard the Mars Global Surveyor (MGS) spacecraft during the period known as Science Phasing Orbits (SPO). The frequency of these waves, measured in the MGS reference frame (SC), is close to the local proton cyclotron frequency. Minimum variance analysis (MVA) shows that these ‘proton cyclotron frequency’ waves (PCWs) are characterized – in the SC frame – by a left-hand, elliptical polarization and propagate almost parallel to the background magnetic field. They also have a small degree of compressibility and an amplitude that decreases with the increase of the interplanetary magnetic field (IMF) cone angle and radial distance from the planet. The latter result supports the idea that the source of these waves is Mars. In addition, we find that these waves are not associated with the foreshock and their properties (ellipticity, degree of polarization, direction of propagation) do not depend on the IMF cone angle. Empirical evidence and theoretical approaches suggest that most of these observations correspond to the ion–ion right hand (RH) mode originating from the pick-up of ionized exospheric hydrogen. The left-hand (LH) mode might be present in cases where the IMF is almost perpendicular to the Solar Wind direction. PCWs occur in 62% of the time during SPO1 subphase, whereas occurrence drops to 8% during SPO2. Also, SPO1 PCWs preserve their characteristics for longer time periods and have greater degree of polarization and coherence than those in SPO2. We discuss these results in the context of possible changes in the pick-up conditions from SPO1 to SPO2, or steady, spatial inhomogeneities in the wave distribution. The lack of influence from the Solar Wind's convective electric field upon the location of PCWs indicates that, as suggested by recent theoretical results, there is no clear relation between the spatial distribution of PCWs and that of pick-up ions.