The present phase of the Human Genome Project is concerned with sequencing. The shift of emphasis has left an impression that mapping is in some sense complete or finished. On the contrary, faced with the challenges of mapping genes for complex traits and efforts to understand recombination and other biological processes, the need for accurate integrated metric maps is greater than ever. Furthermore, sequencing could be regarded as merely a way of improving the map, since the most useful ‘end product’ of the sequencing effort must be the annotated sequence that gives precise physical coordinates for markers and expressed sequences. Integration of both location and functional information, the latter provided by homology, expression and other functional studies, is the main target for the future.