While working in the late 1970s in the European Molecular Biology Laboratory, Heidelberg, Wieschaus collaborated with Christiane Nüsslein-Volhard on a study of the genetic factors producing segmentation in the fruit fly Drosophila melanogaster. Flies were exposed to mutagenic chemicals and thousands of their larval descendants examined to see if particular types of mutants emerged. Their work, published in 1980, established 15 mutant loci that radically altered the segmental pattern of the Drosophila larvae. It allowed the main development sequences to be marked out – to show, in effect, how the embryo becomes increasingly segmented. At first the gap genes divide the embryo into its main regions. Pair-rule genes then subdivide these regions into segments and, finally, polarity genes mark out repeating patterns in each segment. This has proved to be especially significant as it is suspected that the same development pattern may be found in other organisms. It has even been suggested that Waardenburg's syndrome, a rare disease in humans that leads to deafness and albinism, is caused by mutations in the human version of the pair-rule gene.

Wieschaus shared the 1995 Nobel Prize for physiology or medicine with his collaborators Nüsslein-Volhard and Edward Lewis.