The most impressive structure at Sesklo is the so-called 'megaron' (1-2-3-4-5-6) excavated by Christos Tsountas in the early twentieth century. Built in the Late Neolithic on the highest point of the hill, it was surrounded by circular stone enclosures separating it from the other houses of the settlement, which were smaller and simpler.

The building is orientated east-west and consists of a porch (1), a main chamber (2) and a back room (3). The entrance door is located on the west wall. The building had stone foundations, brick walls and a timber roof. The large main chamber was almost square in shape, with a clay floor and a square clay hearth. Three conical holes in the middle of the floor held the wooded poles supporting the roof. At the northwest side of the chamber are two small oblong structures of stone, which were related to household activities. A separate trapezoid area east of the 'megaron' was turned later into a back porch.

Today, only the stone foundations are preserved, while part of the building, including the southeast side of the yard that surrounded the house collapsed into the adjacent stream. Nonetheless, the Sesklo 'megaron' remains the most impressive structure of the Neolithic period in the whole of Thessaly.