The geophysical mapping of the Neolithic Settlement of Kandou- Kouphovounos, in Cyprus, was conducted as part of the continuing archaeological research program in the specific area. The goals of the project included the mapping of the shallow depth architectural remains of the site in order to assess the limits of the settlement and plan the future excavations of the site. Magnetic surveying was successfully applied, together with soil resistivity prospecting. Both techniques resulted to a number of features that have been correlated to the existence of architectural features. The electromagnetic survey (EM38) encountered various problems related to the balancing of the instrument due to the extreme high temperatures, the high resistivity of the shallow bedrock and the lack of contact with the surface due to the dense vegetation islets and bedrock outcrops that were scattered in the area. The magnetic susceptibility maps, covering an area with existing architectural relics, resulted to a detail mapping of their inner details, in close correlation to the other techniques. Subsequent excavations in the following year revealed a number of architectural features which were located by the use of geophysical prospection techniques. The geophysical maps indicate that the site extends in the north, south and west directions with no evidence of a surrounding defensive structure. Further geophysical work is planned to map the relics on the slope of the hill. The final product will consist of the superposition of the excavated regions on the geophysical maps to provide a tool for the management and preservation of the site and its environmental settings.