Using the fruit fly (Drosophila melanogaster) as a model system, she revealed molecular mechanisms underlying the determination of the major axis of the embryo.
Performing genetic screens, she identified mutants that result in female sterility of which many affect embryonic body patterning.
[1] By that, she contributed to the understanding of maternal factors that are deposited into the forming egg during oogenesis and that are conferred into spatial information within the developing embryo to demarcate distinct functional regions.
[3] Genetic screenings for maternal effect "grandchildless" mutants resulted in the identification of a set of genes that are essential for the patterning of the egg and developing embryo.
Many of the affected genes were named by Trudi Schüpbach after royal dynasties that extinguished due to the lack of offspring such as staufen, vasa, valois and tudor.