According to the spirit of Dr. Leite de Vascconcelos, founder and first director of the MNA, the Museum should display “a permanent exhibition of objects of all periods of our civilisation, from the remotest times, origins, life and characteristics of the Portuguese People”. The size and diversity of the Museum’s Collection must be understood in this context, distributed by difference groups: archaeology, ethnography, numismatics and medals, pre-Latin and Latin epigraphy, sculpture, mosaics, physical anthropology, and the famous “comparative collections”, archaeological and ethnographic, made up from materials from various countries and continents. 
The uniqueness of the various groups demanded the creation of specific reserve collections, according to the material nature of the objects, conservation demands and environmental control:

 - Ethnographic reserve colletion
 - Amphorae reserve collection
 - Metal artefacts reserve collection (goldwork, coins and medals, and other metal objects) 
 - Mosaic reserve collection
 - Stelae reserve collection  (epigraphy, sculpture, and other stonework)

The large collections of the MNA (the largest “archaeological site of the country”) presents specific problems of inventoring and cataloguing. The earliest inventories of the MNA are made up of three books full of entries, belonging respectivelly to Leite de Vasconcelos, Manuel Heleno and Manuel Viegas Guerreiro, and a general inventory composed by individual entries numbering a total of 75 000. Since this constitutes but a small number of the objects housed in the Museum, the systematic inventory and cataloguing of this imense collection becomes a priority. A basic reference inventory centered around archaeological sites has been created, as well as a cataloguing system for the various groups of objects – the Collection Catalogues. 
This information accessible on-line, is being done through a programme of the Património Móvel dos Museus, also known as Programa Matriz.