In his teaching at the Collège de France, Jean Guilaine dealt with various general problems concerning protohistoric societies (from the Neolithic to the Iron Age), illuminating them with a diversity of examples and the documentation of his own research. Thethemes covered were : Neolithic historiography, human representations and gender, symbols and societies in recent prehistory, Mediterranean hypogeism, ancient Mediterranean protohistory : islands and continents. Seminars provided updates on the latest developments in research into the global cradles of agriculture, the emergence of megalithism, the use of certain materials in symbolic coding and social functioning, the processes of chalcolithization, human impact on the environment, and funerary rites as evidence of social hierarchization. These seminars have been the subject of eleven books published by Editions Errance.

Jean Guilaine's theoretical analyses covered a range of topics : the concept of arrhythmia in the diffusion of the European Neolithic, the need for environmental archaeology and the processes of anthropization, prehistoric violence and warfare, the diversity of megalithisms and hypogeisms, the Campaniform phenomenon, Neolithic iconography and gender, the rhythms of Mediterranean history over the long term, metal hoarding and West Mediterranean networks in the Iron Age. Several of these themes have been summarized in various works.

A man of the field, Jean Guilaine has directed or co-directed excavations in Cyprus, Greece, southern Italy, southern France, Andorra and Spain. His work has led to the publication of multi-disciplinary monographs, all of which are case studies shedding light on the protohistory of the Mediterranean from the ^10th to the ^1st millennium BC.