Naqada comprises some villages such as Tukh, Khatara, Danfiq and Zawayda. It stands near the site of a necropolis from the prehistoric, pre-dynastic period around 4400–3000 BC. Naqada has given its name to the widespread Naqada culture that existed at the time, here, and at other sites including el Badari, Gerzeh and Nekhen (Hierakonopolis). The large quantity of remains from Naqada have enabled the dating of the entire culture, throughout Egypt and environs.
The town was the centre of the cult of Set, and large tombs were built there around c. 3500 BC.