Down syndrome (MIM 190685) is the most common genetic form of mental retardation. It is caused by trisomy of all or a portion of chromosome 21. The 2.5-Mb region [3, 4] between DNA markers D21S17 and ERG (MIM 165080) is associated with the main features of Down syndrome and is termed the Down syndrome critical region. As part of the human genome project, our laboratory is studying the physical structure of human chromosome 21. To identify the genes and functional units mapped on chromosome 21, we are focusing on the physical mapping and sequencing of several regions. One region we have sequenced is the distal 1.6-Mb end of the Down syndrome critical region. The 4-Mb region from the SOD1 gene (MIM 147450) to the AML1 (MIM 151385) gene will soon be completely sequenced. This study describes the detailed sequence analysis of these two regions of chromosome 21.