At a first glance, the lens eyes of mammals and compound eyes of insects seem to have nothing in common except that they sense the light. Therefore, one of the most striking surprises in modern biology was the demonstration that the expression of a mouse gene required for eye formation can induce an insect eye when expressed, from a transgene, in the fruitfly Drosophila (Haider et al., 1995). Prior to this demonstration of a “universal master control gene”, developmental biologists had already shown that transcription factors of the Hox, Pax, zinc finger and forkhead class are conserved in evolution (e.g. Sharkey et al., 1997; Noll, 1993; Pieler and Bellefroid, 1994; Lai et al., 1993) and that the same signaling molecules and signal transduction systems participate in cell-cell communication events underlying pattern formation and organogenesis of all animals (e. g. Cadigan and Nusse, 1997; Padgett et al., 1998; Tan and Kim, 1999). These findings made scientists start acting as if the proper study of mankind is a combination of sequencing the human genome and an understanding of gene functions in model organisms such as yeast, nematode, fly, frog, zebrafish and mouse. Here we review the Drosophila system as a model showing that sophisticated genetics, developed over a period of a century, as well as its advanced molecular biology make this organism best suited for the study of functional genomics and for addressing basic questions in metazoan biology.