We show here that the method of genomic denaturing gradient electrophoresis (gDGGE) can be used to examine any gene that has been previously cloned and sequenced, and to detect and approximately localize within the gene the majority of its polymorphisms. By using pooled-DNA gDGGE, many different samples can be scanned on a single gel. Further, the patterns on the gels and results from sequencing of some of the alleles shows that a variety of different kinds of polymorphism, ranging from single base changes to more substantial allelic differences, can be distinguished. The extramacrochaetae (emc) gene of Drosophila melanogaster exhibits no polymorphism in its ORF that can be detected by this method, although a rearrangement polymorphism was detected in the 3' downstream region of the gene. The suppressor-of-hairless (Su(H)) gene of D. melanogaster, however, exhibits a variety of polymorphisms in its ORF. Some are small deletions or insertions in a glutamine-rich part of the gene product that would not have been detectable by ordinary screening methods. Many of the polymorphisms detected in this preliminary survey are likely to have an impact on the function of the Su(H) gene product.