Human habitation may significantly affect the chemical soil composition leading to enrichments and depletions of specific chemical elements and the formation of archaeological soils. Prospection and interpretation of sites by means of element analysis of soils requires appropriate and well-tested geochemical methodologies. In this paper element analysis in archaeological prospection and site interpretation is briefly reviewed and three major unresolved issues are discussed: (i) how to distinguish archaeological chemical signals in soils from modern and geogenic signals; (ii) what role do geochemical processes play in the formation of archaeological soils; (iii) how to implement geochemical methods in archaeological research programmes. These issues are addressed with reference to the geochemical literature on retention and sequestration pathways of presumed anthropogenic elements in soils and analytical procedures. Based on the acquired knowledge, several directions for future research are proposed. Copyright © 2009 John Wiley & Sons, Ltd.