In 1878, Surgeon General G. Bidie, the then Superintendent of the museum, made Ethnology, (a branch of anthropology) as a museum subject to be illustrated by pre-historic antiquities and ethnographic materials. The Government instructed all district authorities to render assistance to the Superintendent of the Museum concerning Pre-historic Archaeology of the various districts. The collection of pottery/terracotta from the ancient burials of the Nilgiris, known as Breek's Collection, reached the Museum in 1878 AD. Robert Bruce Foote made his first discoveries of early man during this period and the Madras Museum received some of these finds. Dr. Edgar Thurston, successor of Surgeon General G. Bidie published seven volumes of "Castes and Tribes of Southern India" by bringing together a vast body of ethnological information. By about 1890 AD, Thurston began to pay special attention to Ethnology and strengthened the Ethnological Section of the Museum. In 1904-1905 AD, Government purchased Mr. Bruce Foote's pre-historic and proto-historic collections (such as Paleolithic and Neolithic tools, hammer stones, scrapers, bangles and beads from various parts of southern India). For the next hundred years, both the British and Indian scholars and experts were constantly making many such contributions, from time to time.

The life of ancient man in India is depicted by a wealth of artifacts of stone, copper, bronze and iron ages. The Pre-historic antiquities include the large classical collections made and catalogued by the pioneers of prehistoric studies in India, such as J.W. Breeks, Robert Bruce Foote, Alexander Rea. World famous collections of tools, pottery, ornaments, beads, weapons, agricultural implements, utensils, ritual objects, urn burials and stone monuments belonging to the Paleolithic, Mesolithic and Neolithic age of India help us in understanding the culture of the ancient Deccan and Peninsular India. Alexander Rea's Adichanallur collections of stone, terracotta, bronze and iron, which are about 3200 years old, are remarkable. Adhichanallur artifacts such as, burial urns, potteries, articles of ritual use, ornaments, agricultural tools, household articles and weapons made of metals testify that one of the earliest civilizations of the world thrived in Tamil Nadu. The Museum's prehistoric artifacts excavated from, the over five thousand-year-old, Indus valley civilization throws light on the life of Indus people.

A number of cannons captured at Manila, Mysore and Tranquebar, large series of matchlocks, musketoons, handguns, blunderbusses, rifles and pistols used by the English East India Company or captured by them as war trophies are in the collection. A very large and varied collection of ceremonial and lethal weapons such as gauntlets swords, daggers, maces, elephant goads, choppers, knives, shields, spears, halberds and pikes obtained from the Tanjore Armory are the other important weapons. Several of these arms have exquisitely carved designs of Yalis, Makaras and Parrots on them.

The ethnographic collections represent the material culture of South Indian ethnic people such as Chenchus, Gadabas, Khonds, Kotas, Lambadis, Savaras and Todas. The ethnic and folk collections such as hut models, implements of hunting/agriculture, weapons, fire-making implements, writing materials, cult objects, ornaments, jewels, folk dance figures of Tamilnadu, Kathakali figures, folk and fishermen deities, votive offerings to gods and goddess, sorcery figures, Kondapalli toys, Meriah's sacrificial post, shadow play figures and toys explaining mythical concepts, bring out various nuances in the culture of Indian folks. Stringed, wind and percussion musical instruments from various parts of India are also there.

Physical or biological anthropology deals with the evolution of humans, their variability, and adaptations to various environmental stresses. The museum's specimens pertaining to the Physical anthropology give knowledge about various human ethnic groups, evolution of humans from apes and gradual spread to various parts of the world out of Africa.