The distribution of the sites shows that the first farming and stock-rearing settlements were situated in coastal or inland areas, lowlands or hilly, close to water sources (lakes, rivers, streams, springs). In their majority they were open settlements, while cave-dwelling has also been recorded, especially during the last phases of the Neolithic.
The density of the settlements differed according to regions. For example, the large fertile plains of Thessaly and Macedonia were more densely populated than the semi-mountainous regions of southern Greece and the islands. In addition, the density of the settlements did not remain the same throughout all the Neolithic phases. Local geomorphological changes, such as a rise in the sea level, as well as natural disasters, such as the overflowing of rivers, had a direct impact on economy and determined the further settlement behaviour of Neolithic man.

Open settlements had usually the form of a low hill, 2-4 metres high, with a diameter of 100-200 meters. In the Thessalian plain they were known by the name "magoula", while in Macedonia they were given the term "toumba" which is a corruption of the word "tymvos" (tomb). These hills were not natural elevations of the ground, but were created by succesive habitation layers on the same spot over hundreds or even thousands of years.

The size of the Neolithic settlements is not known, since none of the known settlements so far have been thoroughly excavated. From the most fully investigated settlements (e.g. Sesklo, Dimini, Makriyialos) we can conclude that their size ranged from 500-6,000 square metres. The first farming and stock-rearing communities are estimated to have numbered 100 to 300 individuals.

The organization and architectural structure of the settlements differed according to regions and periods. During the Early Neolithic, settlements consisted of huts with walls made of posts, while from the Middle Neolithic onwards houses with stone foundations and walls from mud-bricks (unfired bricks from a mixture of clay and hay) were built. Houses were one-room or additionally posessed an open or closed porch ("megaron-type"). They were built independently of each other, on the ground floor as a rule, while there are indications that two-storey dwellings existed as well. Several settlements were surrounded by ditches or stone enclosures (e.g. Argissa, Dimini), whose function is not entirely clear: for defense or to demarcate the limits of the settlement?