We have previously isolated a 500 bp-long cDNA clone, NO9-15, which is derived from a nuclear transcript originating from the heat shock locus 2-48B of Drosophila hydei (Peters et al. 1982). Sequence analysis shows that this clone carries 4 complete copies and 1 partial copy of a 115 bp repeat unit. The repeats are closely homologous with a maximal sequence divergence of about 10%. The sequence does not contain an open reading frame. The genomic organization of heat shock locus 2-48B, as probed with the cloned cDNA sequence NO9-15, is highly polymorphic. Four different allelic arrangements have been found in different inbred strains. A number of genomic clones isolated from region 2-48B, both in phage lambda and in cosmid vectors, all differ in length, mainly due to varying numbers of the NO9-15 repeat unit. These differences are found primarily in the proximal region of the locus. The transcribed region of these clones includes the distal sequence flanking the NO9-15 repeat as well as the NO9-15 repeat itself. An oligo A stretch was found between the distal flanking sequence and the NO9-15 repeat region.