The oldest remains of human activity on the Skopje Kale are directly associated to archaeological deposit of the area, which was formed through long geological processes, on the base of sedimentary sandbar. First of all, thick layer of river alluvium was formed, or more precisely, a type of a pebble stone river terrace was created. Through washing a layer of sand clay with a sedimentary base was deposited on it. This clay layer, somewhere red, somewhere yellow, appears with a thickness se greater than one meter. Precisely this sand clay reveals the various dug in items, such as the remains of the initial – oldest settlement from the Copper Age-Eneolithic Age or from the 4 millennium before Christ.
These are mudhuts or semi-mudhuts, functioning as habitats, then there are cult objects or waste or storage pits. Their inventory is usual for this type of objects and is consisted of numerous forms, such as ceramic pots for various use, cult items, clay sculptures, but also tools and cutters made of bone, stone and flint. Their intensity, disposition and organization speak of a large and economically strong settlement which encompassed the entire area of the Kale and the first eastern terraces.
All points researched as low as the clay deposit without exception reveal Eneolithic finds, always in immediate relation to the deposit. The most well and most completely preserved such remnants were discovered Sectors 3A and 7, or where there was a lower intensity of space utilisation in the younger ages.
In the layer of yellow sand clay in Sector 7, parts of 4 semi-mudhuts were discovered. The situation is similar in Sector 3A as well - the only wider and more appropriate space for prehistoric research which was not significantly covered by the later buildings. This is where 2 subsequent Eneolithic phases were found. In the older phase this space was used as cult section of the settlement or area for satisfaction of the religious needs of the population in the early Copper Age. In the areas within a circular border various ritual and religious activities were performed with sacrificial offerings and their leaving there, or to be more precise, gathering of their residues in some sort of cult pits, vertically dug into the clay subsoil. These objects had a section above the surface made of skeleton construction with rammed in poles and a lower, vertically dug in section in the shape and with the content of a cult pit. In the following phase, the same area supported houses with rectangular towards elliptic foundation, that is, with a floor dug into the clay subsoil at about 20 cm. The section above the ground had a tent shape and roof on two posts.
Throughout the following period of the Bronze Age or in the course of the III and II millennium before Christ, the prehistoric living resumed, however, on a smaller area, limited mainly to the north-eastern sections of the Kale. Consequently most of the Bronze Age layers were discovered only in Sector 7. These document, beside the numerous mobile finds, remains of kilns for ceramics from the early Bronze Age, parts of housing objects from the middle Bronze Age and a house from the late Bronze Age. All of these speak of continuous development of a local culture in which the general Balkan values were observed, the ones from the so-called along-the-Danube-Balkan cultural complex. Still, towards the end of the Bronze Age there is an evident presence of elements from the south (mostly in the ceramics) which, just as the entire Vardar valley area, culture-wise turns this area towards the Aegean south.
The youngest prehistoric settlement, the one from the Iron Age (first half of the first millennium before Christ) meant continuation of the life; however it was now focused on a new position, mainly in the south-eastern sections of the Kale. Although taking up a very small area, there were remains of the common prehistoric architecture or houses on rectangular foundation, built with skeleton construction made of poles and adobe. Their inventory mainly includes ceramics, common for the Iron-Age culture in Macedonia.