Forty-three yeast artificial chromosomes (YACs) from the X chromosome have been overlapped across the 4-Mb Xq21.3 region, which is homologous to a segment in Yp11.1. The region is formatted to 60-kb resolution with 57 STSs and is merged at its edges with contigs specific for X. This allows a direct comparison of marker orders and distances on X and Y. In addition to some sequence variation and possible differences in marker order, two larger evolutionary divergencies between the X and Y homologs were revealed: (1)) The X homolog is interrupted by a small X-specific region detected by a 3-kb plasmid probe for locus DXS214. An STS was developed from one end of the probe, but the sequence at the other end was highly homologous to an L1 repetitive element. This suggests that the interpolation of the X-specific segment may have involved an L1-mediated event. (2) A 25O-kb portion containing DXYS1 is several megabases away from the rest of the homologous DNA on the Y but is contiguous with the remainder of the homologous region on X. Marker orders are consistent with the origin of the Y-specific 250-kb region in a paracentric inversion after the initial transfer of X DNA to the Y chromosome.