It has been previously reported that the abundance and distribution of transposable elements (TEs) in Drosophila heterochromatin are conserved in unrelated stocks although they may greatly differ between families. The biases in genomic distribution of TEs are potentially informative for understanding host-transposon interactions. Here we report that in most stocks, one to four elements of the 1731 retrotransposon family are located on the Y chromosome within regions that appear to be polytenized in larval salivary glands. We discuss the hypothesis that these elements may be beneficial to the host and consider the relevance of our observations to the organization of sequences within the heterochromatin.