The "selfish DNA" theory postulates that transposable elements (TEs) are intragenomic parasites, and that natural selection against deleterious effects associated with their presence is the main force preventing their genomic spread in natural populations. In agreement with this model, TEs in Drosophila melanogaster populations are usually found at low frequencies in most genomic locations. Only a few cases of fixation of TE insertions have been reported, usually in regions of low recombination, where selection is expected to be less effective. Here, we report a population genetics study on the apparent fixation of an S-element in a highly recombining region in two natural populations of D. melanogaster. Three similar fragments of an S-element are inserted into the 5' regions of three members of a heat shock gene family, Hsp70 (Hsp70Aa and Hsp70Ab in polytene chromosome band 87A, and Hsp70Bb in 87C). A PCR-based analysis suggests that the insertions are fixed or at high frequencies in the entire species. A population survey of the levels of nucleotide sequence variation at the insertion site in 87C in two natural populations of D. melanogaster provided evidence for reduced levels of variation in the region, normal levels of recombination, and selection, reflected in a significant departure from neutrality of the variant frequency spectrum. This was particularly strong for the S-element inverted repeats (IRs) and suggests that these are of functional significance for the host.