We have previously identified YACs containing the Y breakpoint in a male patient with Turner-like hydrops in the newborn period and a Y;16 translocation (Erickson et al., 1995). We have now subcloned these YACs and built a lambda contig across the Y breakpoint. A subclone near the Y;16 breakpoint of our patient shows great evolutionary conservation by hybridization to a zoo blot. We have sequenced the region responsible for the hybridization and found a foamy (spuma) virus sequence. These viruses are known to be xenotropic and a very similar cross-species hybridization (using the same commercial zoo blot) was recently reported with a human foamy virus clone (Cordonnier et al., 1995). Thus, we have identified a foamy virus insertion near the Y heterochromatin boundary.