Controversy abounds around the presence of Palaeolithic man in Malta.  A number of cave drawings and microliths, together with the presence of two taurodonts in a Pleistocene deposit and results from uranium dating are all pointers towards the possibility of Palaeolithic man living in Malta. Uncertainty regarding the interpretation of the evidence provided by the above has however divided Maltese scholars, and to date no definite conclusion has been reached.

On a more secure ground, it is thought that man arrived on the islands around the year 5200 BC.  The first Neolithic culture shows great affinity to that of Monte Kronio in  Sicily and later in at least one location ( i.e. the Mixta Caves in Gozo ) , the local culture appears to have had contacts with the eastern Sicilian cultures of the Middle Neolithic previously grouped under the Stentinello culture.

The earliest people on the islands, after an initial period of seasonal utilization of the archipelago's resources, eventually established themselves in cave and open dwellings and developed into the Ghar Dalam culture.  They grew barley, wheat and lentil, practised fishing and supplemented their food with hunting. Around seven hundred years later this culture evolved into the Grey Skorba culture.  This in itself lasted on the islands for only about a century after which the Maltese were influenced  by the Diana culture. Extending into the Italian Peninsula, eastern Sicily and the Aeolian islands the influence of the Diana culture in Malta is felt through the presence of monochrome red pottery and trumpet lugs, which feature in the last Maltese Neolithic culture namely that of Red Skorba.

The Zebbug and Mgarr phases span the first eight hundred years of the Temple Period, but have not yielded any Temple remains. It is however during these two phases that the inhabitants through confidence in agriculture managed to provide a surplus of food which was essential to sustain a healthy community.  This allowed a group of people to take leadership in ritual and community affairs, thus providing the seeds for social change that shaped later prehistory.  The surrounding sea allowed commercial and cultural contact with Sicily, but also isolated the Maltese islands allowing its inhabitants to evolve on essentially internal inspirations to produce the unique monuments so characteristic of the Temple period.

Beginning in the middle of the fourth millennium BC, the Neolithic people on the Maltese archipelago involved themselves in the construction of places of cult, that remain to date, unparalleled elsewhere in the world.  Each of the forty-two Maltese Temples, with its particular plan belongs to a group of structures that claim to be one of the earliest achievements of mankind.In the book Before Civilization , Sir Colin Renfrew declares that the "earliest architecturally conceived exterior in the world" is probably the facade of the Ggantija Temples on the island of Gozo.  This same temple claims to be  the earliest free-standing structure in the world. On mainland Malta, the temples at Hagar Qim, possess the "earliest use of dressed stone” in human prehistory, while the colossal statue in the Western temple at Tarxien was probably unique for its size at the time.

Temples show a development in form, commencing as niche like spaces gathered around an irregular court and culminating in a symmetrical structure with three pair of apses grouped around a common axis.  This change in the temples' structure parallels the increasing complexity of the Maltese Temple Period society.

After collapse of the Temple culture Malta comes to fall part, albeit late, of the Mediterranean Bronze Age by occupying the south-western tip of a cultural arc which spanned from the Aegean through the Puglia region in Italy and Western Sicily.  Evidence for this cultural migration is provided by the affinity of early Maltese Bronze Age pottery with Protohelladic (Aegean) and Capo Graziano (Aeolian) styles. Bossed bone plaques and clay anchors are also found across this region, while only Puglia and Malta seem to have the remains of the characteristic dolmen of this cultural phenomenon.  The first Maltese Bronze Age culture namely that of Tarxien Cemetery is mostly known for its funerary remains. Traced back to this culture are four types of burial monuments, namely ritualized megalithic temples, menhir, cairns and dolmens.

Influence, and possibly migration, from western Sicilian cultures resulted in the second local Bronze age culture, named after the type site at Borg in-Nadur. These people after a transient coexistence with the Tarxien Cemetery people are soon characterized by settlement patterns that show preoccupation with defence and security.  The last two centuries of Maltese Bronze Age bring with them the Bahrija folk,  who probably occupied areas in western Malta.  At around the middle of the seventh century B.C., Malta becomes part of the Phonicien world through its strategic position in Mediterranean trade routes