In the recent years the measure of the magnetic susceptibility has been proved to be a reliable tool for the monitoring of pollution in topsoils. However the increase of magnetic susceptibility is not always correlated with polluted sources but it is possible to reflect the geological background of the area. In the present study a broad area in the southeast part of Thessaloniki city has been investigated by means of magnetic susceptibility measurements. In total 77 profiles up to 70 cm depth have been sampled. Magnetic susceptibility was measured in two different frequencies (0.47 and 4.7 KHz) and the percentage of frequency dependence was calculated. The spatial distribution of the magnetic susceptibility values was performed using GIS techniques. The results revealed the presence of two areas with high susceptibility values. These areas are investigated in details in order to distinguish the anthropogenic or the lithogenic influence.