In the last decades, geophysical methods such as magnetic survey have become a common technique for prospecting archaeological sites. At sub-Saharan archaeological sites, however, magnetic survey and correlated techniques never came into broad use and there are no signs for an immediate change of this situation. This paper examines the magnetic survey undertaken on the Nigerian site of Zilum, a settlement of the Gajiganna Culture (ca 1800-400 BC) located in the Chad Basin and dated to ca 600-400 BC. By means of the present case study, we demonstrate the significance of this particular type of investigation in yielding complementary data for understanding the character of prehistoric settlements. In conclusion, we point out that geophysical methods should play a more important role in modern archaeological field research, as they furnish a class of documentation not achievable by traditional survey and excavation methods, thus creating new perspectives for interpreting the past of African societies.