The US Department of Energy’s interest in chromosome 5 emerged from a series of pilot studies begun at the Lawrence Berkeley National Laboratory focusing on a cluster of interleukin genes located at human 5q31. These studies of a megabase of chromosome 5 illustrated how finished human sequence could contribute to gene annotation and how multi-mammalian sequence comparisons could lead to the sequence based identification of noncoding elements possessing gene regulatory activities. The finished sequence of chromosome 5, and its analysis alone and in comparison to orthologous regions in other vertebrate genomes now provides a chromosome-wide catalog of genes and evolutionarily conserved noncoding sequences. Many of these insights, as well as clues into disease causing deletions arising from the segmented duplication landscape of chromosome 5, can only now be appreciated with the finished sequence of this chromosome in hand.