The Prehistoric Collection of the Archaeological Museum of Istria was opened to the public in 1973, when the archaeological exhibition from the prehistoric period (Palaeolithic, Neolithic, Bronze and Iron Ages) was presented. Its development began much earlier, in 1902, with the discovery of a rich Iron Age necropolis at the site of Nesactium, which prompted the founding of the museum itself. 

The collection includes finds from the territory of Istria from the Palaeolithic, Mesolithic, Neolithic, Eneolithic, Bronze, and Iron Ages, and it deals with the research of the development of communities in Istria until the arrival of the Romans. 

Its main goal is to preserve, scientifically process, and present the heritage of prehistoric Istria to the public. Through long-term and systematic work, it documents the development of prehistoric communities through material remains such as tools, pottery, jewellery, and weapons. In addition to expert and scientific processing, it collaborates on numerous projects with various institutions and experts, both in Croatia and abroad, with the aim of improving the research, protection, and presentation of archaeological heritage. 

The most numerous finds from the Palaeolithic and Mesolithic periods were collected through systematic and trial archaeological research of speleological sites such as Pupićina Cave, Vela Peć, and Vešanska Cave. One of the most significant is Šandalja, where, among other things, a flint chopper estimated to be around 800,000 years old was found, making it one of the oldest human-made objects in Europe. In addition to these, Romuald's Cave is of great importance, where the first known figurative Palaeolithic paintings in Southeastern Europe were discovered. 

For the Neolithic period, the prominent sites are Vižula near Medulin, Vela Gromača near Kavran, Kargadur, Sv. Mihovil, Ljubićeva Cave, and Laganiši. 

The Bronze Age is marked by archaeological material from numerous hillfort settlements – castellieri – and occupies a significant part of the collection. Important sites for this period are Monkodonja, Vrčin, Sv. Petar – Tondolon, Gradac – Turan, Trogrla Cave, and Cingarela. Among the Bronze Age necropolises and tumuli, the sites of Vrčin, Mušego, and Maklavun stand out.

The Iron Age is represented by finds from urnfield necropolises such as Nesactium, Picugi, Pula, and Kaštel near Buje, while significant individual urn burials have been found at the sites of Sv. Martin and Punta Kašteja. Notable finds include figuratively decorated bronze situlae and imported pottery of South Italian and Greek origin, which testify to the cultural ties of Istria with the Mediterranean world. Of particular value are the fragments of stone sculptures that bear witness to the uniqueness of the Iron Age culture of the Histri, providing insight into their spiritual world and symbolism, and playing an important role in building the identity and cultural heritage of Istria.